🌌 Implementing the Serena MCP Server with Claude Desktop on Windows 11

🌟 1. Introduction

🚀 Welcome to this comprehensive guide! This section will give you the foundational knowledge you need.

⚡ Purpose

This guide provides comprehensive, step-by-step instructions for integrating the Serena AI coding assistant with the Claude Desktop application on a Windows 11 operating system. Serena is designed to interact directly with local codebases, employing semantic understanding to assist with various coding tasks.1 This integration leverages the Model Context Protocol (MCP) server mechanism provided by Serena.

⚡ MCP Role

The Model Context Protocol (MCP) serves as the communication backbone for this integration. Serena implements an MCP server component that acts as a bridge, exposing its advanced functionalities – such as semantic code retrieval, analysis, and modification – as discrete “tools”.1 The Claude Desktop application, acting as an MCP client, can then discover and invoke these tools.

⚡ Target Platform

The procedures detailed herein are specifically tailored for execution on the Windows 11 operating system. While Serena and Claude Desktop may be available on other platforms 1, the installation paths, commands, and configuration file locations referenced in this document pertain exclusively to Windows 11.

⚡ Benefit

The primary objective of this integration is to empower the Claude Desktop application – potentially including the free tier offering 1 – with Serena’s sophisticated code manipulation tools. This enables a more powerful, semantically aware interaction with the user’s local codebase, enhancing Claude’s ability to assist with complex development tasks directly within the user’s environment.1

⚡ Structure

This document is organized into the following sections to guide the user through the complete implementation process:

Prerequisites: Essential software components and versions required before starting the integration.
Serena Project Setup: Downloading the Serena source code.
Serena Configuration: Setting up Serena’s core and project-specific configuration files.
Claude Desktop Configuration: Modifying Claude Desktop settings to recognize and launch the Serena MCP server.
Running and Verifying the Integration: Launching the integrated system and confirming its functionality.
Troubleshooting Common Issues: Addressing potential problems encountered during setup or operation.

🌟 2. Prerequisites

⚡ Overview

Establishing the correct software environment is a critical first step. Failure to install the required components with the specified versions can lead to significant issues during configuration or execution. Particular attention must be paid to the Python version, as Serena has strict compatibility requirements.

⚡ Python Installation (Version 3.11.x)

Requirement: Serena explicitly requires a Python version that is greater than or equal to 3.11 but strictly less than 3.12 (>=3.11, <3.12), as defined in its project configuration (pyproject.toml).4 This means only Python versions within the 3.11 series (e.g., 3.11.0, 3.11.8, 3.11.9) are supported. Python 3.10 and earlier, or Python 3.12 and later, are incompatible and will prevent Serena from functioning correctly.
Installation Steps (Windows 11): 1. Navigate to the official Python website’s download section for Windows.5 2. Download a stable release Windows installer (64-bit recommended for modern systems) for a Python 3.11.x version.6 It is advisable to avoid installations from the Microsoft Store, as these can sometimes lead to complexities with path resolution or permissions needed for command-line tools.9 3. Run the downloaded .exe installer. 4. Crucially, ensure the checkbox labeled “Add python.exe to PATH” or similar is selected during the initial installation screen.7 This step is vital for making Python, pip (Python’s package installer), and subsequently uv accessible from the standard Windows Command Prompt or PowerShell. 5. Consider selecting “Install for all users,” which might place the installation in C:\Program Files\Python311 and require administrator privileges.8 The default installation path is typically within the user’s AppData folder.8 6. Proceed with the installation, accepting default components. Optionally, disable the MAX_PATH length limit if prompted at the end of the installation.9
Verification: 1. Open a new Command Prompt or PowerShell window (to ensure any PATH changes made by the installer are recognized). 2. Execute the command: python —version.8 The output must display a version starting with Python 3.11.. 3. Execute the command: pip —version.8 This should output the version of pip associated with the Python 3.11 installation, confirming it’s also accessible.

⚡ uv Package Manager Installation

Requirement: Serena utilizes uv, a high-performance Python package installer and virtual environment manager written in Rust, for its operations.1 It is explicitly required for running the Serena MCP server command specified later in the Claude Desktop configuration.1 uv itself requires Python version 3.8 or higher 11, a requirement satisfied by the mandatory Python 3.11 installation. The choice of uv likely stems from its significant speed advantages over traditional tools like pip and its integrated capabilities for environment management, package installation, and script execution (uv run), which simplifies the workflow Serena depends on.1
Installation Steps (Windows 11): 1. The recommended installation method involves using a PowerShell script provided by Astral, the creators of uv.11 2. Open Windows PowerShell. Running as Administrator may be required by some system configurations, but it’s advisable to attempt the command first without elevated privileges.12 3. Execute the following command: PowerShell powershell -ExecutionPolicy ByPass -c “irm https://astral.sh/uv/install.ps1 | iex”

.11 The -ExecutionPolicy ByPass flag temporarily allows the downloaded script to run, which might otherwise be blocked by system policy.4. This script will download and install uv, typically placing the executable in a user-specific location like C:\Users\Username.local\bin and attempting to add this location to the system’s PATH environment variable.135.

Verification: 1. Open a new Command Prompt or PowerShell window. This is important for the shell to recognize PATH changes made by the installer. 2. Execute the command: uv —version. This should display the installed version of uv, confirming the installation was successful and the command is accessible.

⚡ Git Installation

Requirement: Git, the distributed version control system, is necessary to download (clone) the Serena project’s source code from its official GitHub repository.1
Installation Steps (Windows 11): 1. Navigate to the official Git website: git-scm.com.14 2. Download the latest stable Git for Windows installer (usually 64-bit).14 3. Run the downloaded installer. 4. During the installation process, it is generally recommended to accept the default settings unless there is a specific reason to change them.17 Ensure that an option related to adding Git to the system PATH or allowing Git to be used from the Command Prompt is selected (this is typically a default behavior). 5. Alternatively, Git can be installed using the Windows Package Manager (winget) via PowerShell or Command Prompt: winget install —id Git. Git -e —source winget.14
Verification: 1. Open a Command Prompt or PowerShell window. 2. Execute the command: git —version.16 The output should display the installed Git version.

⚡ Claude Desktop Application

Requirement: The user must have the Claude Desktop application installed on their Windows 11 system.1 This application serves as the MCP client that will interact with the Serena MCP server. It is available for both Windows and macOS.1 While MCP server support might be available on the free tier of Claude 1, some advanced features or higher usage limits might necessitate a Claude Pro subscription.20
Installation: Users should download and install Claude Desktop from the official source (presumably Anthropic’s website, although direct links were not present in the provided materials).

⚡ Prerequisites Summary Table

For quick reference, the essential software prerequisites are summarized below:

Software	Required Version	Installation Method (Windows 11)	Verification Command	Notes
Python	3.11.x (>=3.11, <3.12)	Official Installer from python.org 5	python —version	Crucial: Check “Add to PATH” 7
uv Package Manager	Latest Stable	PowerShell: `irm https://astral.sh/uv/install.ps1 \	iex` 11	uv —version
Git	Latest Stable	Official Installer from git-scm.com 14 or winget 14	git —version	Needed to clone Serena repository
Claude Desktop	Latest	Official Download (Anthropic)	(Application runs)	Pro subscription may be needed 20

🌟 3. Serena Project Setup

⚡ Cloning the Repository

1. Choose Location: Select a suitable directory on the local filesystem where the Serena project files will be stored. For example, C:\Projects. Avoid directories with overly complex paths or restricted permissions. 2. Open Terminal: Launch a Command Prompt or Git Bash terminal window. 3. Navigate: Change the current directory to the chosen parent location (e.g., cd C:\Projects). 4. Clone: Execute the Git command to download the Serena repository: Bash git clone https://github.com/oraios/serena.git

.1 This command contacts GitHub and downloads the entire source code and project history into a new subdirectory named serena within the current location (e.g., C:\Projects\serena).

After the cloning process completes successfully, navigate into the newly created Serena project directory using the command:

Bash

cd serena

All subsequent configuration steps will assume the terminal’s current working directory is the root of the cloned serena repository (e.g., C:\Projects\serena).

🌟 4. Serena Configuration

⚡ Overview

Serena’s behavior is controlled through configuration files written in YAML (.yml) format. These files define settings related to project analysis, tool availability, and operational parameters. Two primary configuration files require attention for this setup:

1. serena_config.yml: Contains global settings for the Serena instance, particularly relevant when managing multiple projects. 2. myproject.yml (or similar): Contains settings specific to the user’s codebase that Serena will interact with. The use of a two-tiered configuration system allows for separating global Serena behaviors (like project switching logic) from the specifics of individual codebases (like language or ignored files).1 While this provides flexibility, especially for users working across multiple projects, it necessitates careful management of both file types.

⚡ Creating serena_config.yml

1. Copy Template: Within the serena project directory, create the main configuration file by copying the provided template. In Command Prompt, use: DOS copy serena_config.template.yml serena_config.yml

2. Purpose: This file manages global Serena settings, such as enabling dynamic project switching and configuring logging behavior.23

3. Key Options in serena_config.yml:

* enable_project_activation (Default: True): When set to True, this allows the user to instruct Serena (via Claude) to switch between different projects listed in the projects section using an “activate_project” command.23 If enabled, Serena internally manages which tools are active based on the currently selected project’s configuration, as MCP clients like Claude Desktop typically don’t dynamically update their tool lists.23 Keeping the default True offers flexibility, but requires understanding the activation mechanism. Setting it to False simplifies behavior if only one project will ever be used.

* projects: This is a YAML list defining the code projects Serena can potentially work on. Each entry in the list specifies a project in one of two ways 23:

* By .yml file path: Provide a path (absolute or relative to serena_config.yml) to the project-specific configuration file (e.g., myproject.yml). The project’s internal name is derived from the filename without the extension (e.g., myproject).

* By project directory path: Provide the absolute path to the root directory of the user’s code project (e.g., C:/Users/User/Code/MyProject). In this case, Serena expects the project-specific configuration to exist at <project_root>/.serena/project.yml. The project’s internal name is derived from the final directory name (e.g., MyProject).

* gui_log_window (Default: False): If set to True, attempts to open a separate graphical window displaying Serena’s logs. This feature is explicitly not supported on macOS and has known limitations, including potential instability or multiple non-functional windows being opened due to how clients like Claude Desktop might spawn server processes.23 It’s recommended to keep this False unless active debugging is required and the user is aware of the potential issues.

* gui_log_level: Defines the minimum severity level for messages shown in the GUI log window if it is enabled (e.g., 20 for INFO, 10 for DEBUG).23

4. Action: Open serena_config.yml in a text editor. Define the project(s) Serena should be aware of under the projects: list. For an initial single-project setup using the .yml file path method, this might look like:

yaml projects: - myproject.yml

Ensure proper YAML indentation (typically two spaces).

⚡ Creating Project-Specific Configuration (myproject.yml)

1. Copy Template: Create the project-specific configuration file. The most commonly referenced template is myproject.template.yml.1 Use the command: DOS copy myproject.template.yml myproject.yml (> ⚠️ Note: Some documentation mentions myproject.demo.yml 2; users should verify which template exists in their cloned repository version and use that as the source). 2. Alternative Location: If the project directory path method was used in serena_config.yml, this file should instead be created or copied to <project_root>/.serena/project.yml.22 3. Purpose: This file contains parameters specific to the user’s actual codebase, guiding Serena’s analysis and interaction with that particular project.1 4. Key Options in myproject.yml:

project_root: The absolute path to the root directory of the user’s code project (e.g., C:/Users/Username/MyCodeProject). This is a critical setting. Use forward slashes (/) or escaped backslashes (\) for the path. This parameter is optional only if the file is located at <project_root>/.serena/project.yml. The reliance on absolute paths here can make the configuration less portable if the project location changes.
language: Specifies the primary programming language of the project (e.g., python, typescript, java, csharp, rust, javascript, go, ruby). This is essential for Serena to load the correct language server and apply appropriate analysis techniques. Check the template file for any language-specific requirements (e.g., .sln file for csharp).
ignored_paths: A list of file paths, directory names, or patterns (using standard .gitignore syntax) relative to the project_root that Serena should ignore during analysis. This complements the project’s main .gitignore file (if ignore_all_files_in_gitignore is true). Useful for excluding virtual environments (venv/, .venv/), build outputs (build/, dist/), temporary files (*.tmp), etc..
excluded_tools: A list of Serena tool names to disable specifically for this project. The recommendation is generally to leave this empty (“) to allow Serena full functionality.2 Disabling tools might be considered for security reasons (e.g., execute_shell_command), although MCP clients typically prompt for user approval before execution.2 The command uv run serena-list-tools can be used to view all available tools and their names.
ignore_all_files_in_gitignore (Default: true): Determines if Serena should automatically ignore files and directories listed in the project’s root .gitignore file. Setting this to true is usually desired behavior.
gui_log_window / gui_log_level: These logging options can also be specified on a per-project basis, potentially overriding the settings in serena_config.yml.24 5. Action: Open myproject.yml (or <project_root>/.serena/project.yml) in a text editor. Carefully fill in the correct project_root (unless using the .serena/ convention) and language. Adjust ignored_paths and excluded_tools as necessary for the specific project.

⚡ Key Serena Configuration Parameters Table

The following table summarizes the most critical configuration parameters across both files:

File	Parameter	Description	Typical Value / Example (Windows)	Reference
serena_config.yml	enable_project_activation	Allow switching projects via Claude command?	True (Default)	23
serena_config.yml	projects	List of project config files or directories Serena can access.	[myproject.yml] or “	23
serena_config.yml	gui_log_window	Show separate log GUI? (Limitations apply)	False (Default)	23
myproject.yml	project_root	Absolute path to the root of the user’s code project.	C:/Users/User/Code/MyProject or C:\Users\User\Code\MyProject
myproject.yml	language	Primary programming language of the project.	python, typescript, java, etc.
myproject.yml	ignored_paths	Additional paths/patterns to ignore (gitignore syntax).	[build/, venv/, *.tmp]
myproject.yml	excluded_tools	List of Serena tool names to disable for this project.	“ (Default - use all tools)	2

🌟 5. Claude Desktop Configuration

⚡ Locating claude_desktop_config.json

Claude Desktop stores its configuration, including settings for MCP servers, in a JSON file named claude_desktop_config.json.

1. Path: On Windows 11, this file is located within the user’s Application Data directory at the following path: %APPDATA%\Claude\claude_desktop_config.json .25 2. Accessing: The easiest way to navigate to this location is to open Windows File Explorer, type %APPDATA%\Claude directly into the address bar, and press Enter. This will open the Claude folder within the AppData\Roaming directory. Look for the claude_desktop_config.json file inside this folder. 3. File Creation: If the Claude directory or the claude_desktop_config.json file does not exist, it may be necessary to run the Claude Desktop application at least once for it to be created.25 Alternatively, the user might need to manually create the Claude folder within %APPDATA% and then create an empty text file named claude_desktop_config.json containing only {}.25 Claude Desktop settings can also be accessed via File > Settings > Developer > MCP Servers > Edit Config, which should open the file.1

⚡ Editing the Configuration File

1. Open: Open the claude_desktop_config.json file using a plain text editor (such as Notepad, VS Code, Sublime Text, etc.).25 2. Structure: The file contains a JSON object. Configuration for MCP servers resides under the mcpServers key, which itself holds an object where each key is a chosen name for a server (e.g., “serena”) and the value is the server’s configuration object.1 3. Add Serena Configuration: Add or modify the mcpServers section to include the configuration for Serena. Based on the Serena documentation 1, the structure should be as follows: JSON { “mcpServers”: { “serena”: { “command”: “C:\Path\To\uv.exe”, // <— REPLACE THIS “args”: } // If other MCP servers were previously configured, ensure ‘serena’ is added correctly // with commas separating entries within the mcpServers object. } // Other Claude Desktop settings (like “globalShortcut”) might exist here. // Ensure the overall JSON structure remains valid. }

⚡ Crucial Path Replacements and Formatting

Correctly specifying the paths in this configuration is paramount and a common source of errors.

command Path: The value “C:\Path\To\uv.exe” is a placeholder and must be replaced with the full, absolute path to the uv.exe executable file on the user’s system.1 This path might be similar to C:\Users\YourUsername.local\bin\uv.exe if installed via the standard script 13, but could differ. Relying on the system PATH environment variable for Claude Desktop to find uv.exe can be unreliable 27; providing the explicit absolute path is the most robust approach.
args Paths:

The placeholder “C:\Path\To\serena\repo” must be replaced with the full, absolute path to the directory where the Serena repository was cloned (e.g., C:\Projects\serena).1
The placeholder “C:\Path\To\project\config.yml” must be replaced with the full, absolute path to the project-specific .yml configuration file created earlier (e.g., C:\Projects\serena\myproject.yml or C:\Users\User\Code\MyProject.serena\project.yml).1

Path Formatting for Windows: As JSON strings require backslashes to be escaped, Windows paths must use double backslashes (\) as separators. Alternatively, forward slashes (/) can often be used and are generally simpler to manage within JSON strings.1 For example: “C:\Users\User\Project” or “C:/Users/User/Project”. Using single backslashes will result in an invalid JSON string or incorrect path interpretation.
Optional Project Path Argument: The final path argument in the args array (pointing to myproject.yml) is technically optional if enable_project_activation is set to True in serena_config.yml.1 If this argument is omitted, Serena starts without a specific project loaded, and the user must issue an “activate_project” command via Claude to select one of the projects defined in serena_config.yml. For initial setup and simplicity, explicitly including the path to the desired project configuration file is recommended.

⚡ Understanding the Command Structure

The configuration tells Claude Desktop how to launch the Serena MCP server:

“command”: Specifies the executable program to run, which is uv.exe.1
“args”: Provides a list of command-line arguments to pass to uv.exe. The sequence uv run —directory /path/to/serena serena-mcp-server /path/to/myproject.yml instructs uv to execute the serena-mcp-server script (which is defined within Serena’s pyproject.toml) within the environment and context of the specified Serena repository directory, using the provided project configuration file to guide its operation.1

The fragility of path configuration in external process launching mechanisms like this cannot be overstated. Claude Desktop’s environment might not perfectly mirror the user’s standard shell environment, leading to issues finding executables or resolving relative paths if absolute paths are not used. Strict adherence to absolute paths and correct formatting is essential for success.

🌟 6. Running and Verifying the Integration

⚡ Saving Configuration

After carefully editing the claude_desktop_config.json file and replacing all placeholder paths with the correct absolute paths using appropriate formatting (escaped backslashes or forward slashes), save the changes to the file.

⚡ Restarting Claude Desktop (Crucial Step)

Applying the new MCP server configuration requires a complete restart of the Claude Desktop application.

1. Check System Tray: Simply closing the main application window is often insufficient, as Claude Desktop typically continues running in the background, accessible via an icon in the Windows system tray (usually located near the clock in the bottom-right corner).1 2. Fully Quit: Locate the Claude icon in the system tray, right-click on it, and select the “Quit” option from the context menu.20 Ensure the application process fully terminates. 3. Relaunch: Start Claude Desktop again from the Start Menu or desktop shortcut.

⚡ Verification

Upon restarting, Claude Desktop will read the updated claude_desktop_config.json and attempt to launch the configured MCP servers.

1. Check for Tools Icon: Observe the chat input area within the Claude Desktop interface. The appearance of a small “tools” icon, often resembling a wrench or hammer, indicates that Claude has successfully detected and connected to at least one MCP server.1 2. Inspect Available Tools: Click on the tools icon. A panel or list should appear, displaying the names of the tools made available by the connected MCP servers.20 If the Serena MCP server started correctly, tools specific to Serena’s functionality should be listed. Examples might include find_symbol, apply_edit, read_file, execute_shell_command, list_symbols_in_file, etc. 3. Tool Naming and Interaction: It is important to understand how to interact with these tools. While the server was configured with the name “serena”, instructing Claude to “use Serena’s tools” is unlikely to be effective.1 Claude’s underlying language model interacts with tools based on their registered names and functional descriptions, not the arbitrary server key used in the configuration file.

⚡ Basic Interaction Test

To perform an initial functional check, try submitting a prompt that would likely require Serena’s capabilities. Examples:

“Read the content of the main README file in my project.”
“Find all occurrences of the variable user_id in the file auth.py.”
“What are the main functions defined in src/main.rs?”

Observe the interaction. Claude should ideally recognize that a tool can fulfill the request and may prompt the user for permission to execute the relevant Serena tool (e.g., read_file, find_symbol). Successful execution and a relevant response indicate the integration is working.

🌟 7. Troubleshooting Common Issues

⚡ Overview

Setting up integrations involving multiple software components, configuration files, and specific paths can sometimes lead to issues. This section outlines common problems and steps to diagnose and resolve them.

⚡ Log Files

Claude Desktop and the MCP servers generate log files that are invaluable for troubleshooting.

Location: On Windows 11, these logs are typically found in: %APPDATA%\Claude\logs.20
Key Files:

mcp.log: Contains general information about MCP connections, including successful handshakes and connection failures between Claude Desktop and the servers.26 Check this first for basic connectivity issues.
mcp-server-serena.log (The filename corresponds to the key used in claude_desktop_config.json, so it will be mcp-server-serena.log based on the recommended configuration): Captures the standard error (stderr) output generated by the Serena MCP server process itself.26 This log is crucial for diagnosing errors occurring within the Serena server during startup or operation, such as Python errors, configuration loading failures, or issues finding the language server.

⚡ Issue: Serena Tools Not Appearing in Claude Desktop

If the tools icon does not appear, or if Serena’s specific tools are missing from the list:

1. Verify Claude Restart: Confirm that Claude Desktop was fully quit via the system tray and then restarted.1 A simple window close/reopen is not sufficient. 2. Inspect claude_desktop_config.json:

JSON Validity: Ensure the file contains valid JSON. Copy-pasting the content into an online JSON validator can help identify syntax errors like missing commas or brackets.
Path Accuracy: Double-check all paths (command for uv.exe, args for Serena repo and project config).1 Are they absolute? Do they point to the correct locations?
Path Formatting: Verify that backslashes are correctly escaped (\) or that forward slashes (/) are used consistently.1
Manual Test: Try running the exact command and args specified in the JSON file directly in a Command Prompt or PowerShell window. For example: C:\Path\To\uv.exe run —directory C:\Path\To\serena\repo serena-mcp-server C:\Path\To\project\config.yml. Observe if any errors are printed to the console. This isolates whether the server itself can start outside of Claude Desktop. 3. Check Serena Configuration Files (serena_config.yml, myproject.yml): Ensure these files exist, are valid YAML, and contain correct settings, especially project_root and language in the project-specific file. Errors here could prevent the server from initializing properly. 4. Verify Prerequisites: Re-confirm that the correct Python 3.11.x version is installed and accessible via python —version.4 Confirm uv is installed and accessible via uv —version.11 5. Examine Logs: Check mcp.log for connection errors and, more importantly, mcp-server-serena.log for any error messages generated by the Serena server process during its startup attempt.26 Error messages like ENOENT (Error NO ENTity) often indicate that a specified file or command (like uv.exe or a script it tries to run) could not be found at the provided path.27

⚡ Issue: Tool Name Collisions

Serena provides tools for common tasks like file system operations (read_file, write_file) and potentially shell execution (execute_shell_command). If other MCP servers that offer tools with the exact same names are also configured in claude_desktop_config.json (e.g., the common @modelcontextprotocol/server-filesystem), it can lead to conflicts and unpredictable behavior, as Claude Desktop might invoke the wrong server’s tool.1

Known Conflict: Serena’s documentation explicitly warns about incompatibility with @modelcontextprotocol/server-filesystem due to such tool name collisions.1
Resolution: Since Serena includes file system capabilities, the @modelcontextprotocol/server-filesystem may be redundant. It is recommended to remove the configuration block for conflicting servers from claude_desktop_config.json, leaving only the “serena” configuration (and any other non-conflicting servers).3 Remember to fully restart Claude Desktop after modifying the configuration.

⚡ Issue: gui_log_window Problems

If the gui_log_window: True setting was enabled in either serena_config.yml or myproject.yml and is suspected of causing instability, errors, or multiple confusing log windows:

Resolution: Edit the relevant Serena configuration file(s) and set gui_log_window: False.23 This disables the separate log window feature, which has known limitations and platform incompatibilities.23 Rely on the file-based logs in %APPDATA%\Claude\logs for debugging instead.

⚡ Issue: Permission Errors

While less commonly documented for this specific setup, standard file system permission issues could arise:

Symptoms: Errors related to reading project files, writing files (if using tools like apply_edit), or executing uv.exe or Python.
Checks: Verify that the user account running Claude Desktop has read permissions for the Serena repository directory, the uv.exe location, and the Python installation directory. Crucially, ensure it has read and write permissions for the target project_root directory specified in myproject.yml.

⚡ Checking Serena GitHub Issues

If persistent issues arise that are not covered above, consult the official Serena project’s issue tracker on GitHub: https://github.com/oraios/serena/issues. Search for existing issues that match the problem or consider opening a new issue with detailed information about the setup (OS, versions, configuration, logs).31 Note that at the time of the underlying research, no open issues specifically related to Claude Desktop on Windows were found.31

🌟 8. Conclusion

⚡ Summary

This guide has detailed the process for integrating the Serena MCP server with the Claude Desktop application on Windows 11. The key steps involved installing prerequisites (specifically Python 3.11.x, uv, and Git), cloning the Serena repository, meticulously configuring both Serena’s YAML files (serena_config.yml, myproject.yml) and Claude Desktop’s JSON file (claude_desktop_config.json) with correct absolute paths and formatting, and finally verifying the integration by restarting Claude Desktop and observing the availability of Serena’s tools.

⚡ Next Steps

With the integration successfully established, users can begin exploring the enhanced capabilities of Claude Desktop powered by Serena. Experiment by providing Claude with various coding tasks related to the configured project, such as code analysis, refactoring, documentation generation, or simple code implementation. Observe how Claude utilizes the available Serena tools (often requiring user approval for execution).

⚡ Disclaimer

Software projects like Serena and Claude Desktop are under active development. Installation procedures, configuration file formats, command names, and version requirements may change over time. While this guide reflects the process based on available information, users should always refer to the latest official documentation from the Serena project 1 and check relevant CHANGELOG.md files 1 when installing or updating to ensure compatibility and access to the most current instructions.

🔧 Works cited

1. oraios/serena: a powerful coding agent with semantic … - GitHub, accessed on April 9, 2025, https://github.com/oraios/serena 2. serena/README.md at main - GitHub, accessed on April 9, 2025, https://github.com/oraios/serena/blob/main/README.md 3. Fully Featured AI Coding Agent as MCP Server : r/ClaudeAI - Reddit, accessed on April 9, 2025, https://www.reddit.com/r/ClaudeAI/comments/1jpavtm/fully_featured_ai_coding_agent_as_mcp_server/ 4. serena/pyproject.toml at main · oraios/serena · GitHub, accessed on April 9, 2025, https://github.com/oraios/serena/blob/main/pyproject.toml 5. Download Python | Python.org, accessed on April 9, 2025, https://www.python.org/downloads/ 6. Python Releases for Windows, accessed on April 9, 2025, https://www.python.org/downloads/windows/ 7. Installing Python on Windows 11, accessed on April 9, 2025, https://www.pythonguis.com/installation/install-python-windows/ 8. How To Install Python on Windows | phoenixNAP KB, accessed on April 9, 2025, https://phoenixnap.com/kb/how-to-install-python-3-windows 9. How To Install Python on Windows 10 and 11 | Tom’s Hardware, accessed on April 9, 2025, https://www.tomshardware.com/how-to/install-python-on-windows-10-and-11 10. How to install Python 3 and set up a programming environment for windows 11 pro, accessed on April 9, 2025, https://www.digitalocean.com/community/questions/how-to-install-python-3-and-set-up-a-programming-environment-for-windows-11-pro 11. uv - PyPI, accessed on April 9, 2025, https://pypi.org/project/uv/ 12. Python UV: The Ultimate Guide to the Fastest Python Package Manager - DataCamp, accessed on April 9, 2025, https://www.datacamp.com/tutorial/python-uv 13. Installation | uv - Astral Docs, accessed on April 9, 2025, https://docs.astral.sh/uv/getting-started/installation/ 14. Downloading Package - Git, accessed on April 9, 2025, https://git-scm.com/downloads/win 15. 1.5 Getting Started - Installing Git, accessed on April 9, 2025, https://git-scm.com/book/en/v2/Getting-Started-Installing-Git 16. Git Guides - install git - GitHub, accessed on April 9, 2025, https://github.com/git-guides/install-git 17. How to Install Git on Windows 11 in 2025 ☑️ | Latest Step-by-Step Guide - YouTube, accessed on April 9, 2025, https://www.youtube.com/watch?v=coIOZNCA6TU 18. How to Install Git on Windows - phoenixNAP, accessed on April 9, 2025, https://phoenixnap.com/kb/how-to-install-git-windows 19. Install Git for Windows | Simple Steps for Beginners - Simplilearn.com, accessed on April 9, 2025, https://www.simplilearn.com/tutorials/git-tutorial/git-installation-on-windows 20. My Claude Workflow Guide: Advanced Setup with MCP External Tools : r/ClaudeAI - Reddit, accessed on April 9, 2025, https://www.reddit.com/r/ClaudeAI/comments/1ji8ruv/my_claude_workflow_guide_advanced_setup_with_mcp/ 21. Use Claude Desktop and MCP Servers to Automate Your Desktop & Coding Workflow. | by Mike Knebel | Medium, accessed on April 9, 2025, https://medium.com/@mknebel/how-to-automate-your-workflow-wtih-claude-desktop-and-mcp-servers-5072844b86d1 22. serena/llms-install.md at main - GitHub, accessed on April 9, 2025, https://github.com/oraios/serena/blob/main/llms-install.md 23. serena/serena_config.template.yml at main · oraios/serena · GitHub, accessed on April 9, 2025, https://github.com/oraios/serena/blob/main/serena_config.template.yml 24. myproject.demo.yml - oraios/serena - GitHub, accessed on April 9, 2025, https://github.com/oraios/serena/blob/main/myproject.demo.yml 25. claude-desktop-setup.md - aliargun/mcp-server-gemini - GitHub, accessed on April 9, 2025, https://github.com/aliargun/mcp-server-gemini/blob/main/docs/claude-desktop-setup.md 26. For Claude Desktop Users - Model Context Protocol, accessed on April 9, 2025, https://modelcontextprotocol.io/quickstart/user 27. Using Claude Desktop to Access the Token API via MCP | Docs - The Graph, accessed on April 9, 2025, https://thegraph.com/docs/en/token-api/mcp/claude/ 28. Getting MCP Server Working with Claude Desktop in WSL - Scott Spence, accessed on April 9, 2025, https://scottspence.com/posts/getting-mcp-server-working-with-claude-desktop-in-wsl 29. Claude Desktop - Docs - Appwrite, accessed on April 9, 2025, https://appwrite.io/docs/tooling/mcp/claude 30. MCP Servers Object Structure - LibreChat, accessed on April 9, 2025, https://www.librechat.ai/docs/configuration/librechat_yaml/object_structure/mcp_servers 31. Issues · oraios/serena - GitHub, accessed on April 9, 2025, https://github.com/oraios/serena/issues

Implementing The Serena MCP Server With Claude Desktop On Windows 11

📖 Reading Mode

📖 Table of Contents

🌌 Implementing the Serena MCP Server with Claude Desktop on Windows 11

🌟 1. Introduction

⚡ Purpose

⚡ MCP Role

⚡ Target Platform

⚡ Benefit

⚡ Structure

🌟 2. Prerequisites

⚡ Overview

⚡ Python Installation (Version 3.11.x)

⚡ uv Package Manager Installation

⚡ Git Installation

⚡ Claude Desktop Application

⚡ Prerequisites Summary Table

🌟 3. Serena Project Setup

⚡ Cloning the Repository

⚡ Directory Navigation

🌟 4. Serena Configuration

⚡ Overview

⚡ Creating serena_config.yml

⚡ Creating Project-Specific Configuration (myproject.yml)

⚡ Key Serena Configuration Parameters Table

🌟 5. Claude Desktop Configuration

⚡ Locating claude_desktop_config.json

⚡ Editing the Configuration File

⚡ Crucial Path Replacements and Formatting

⚡ Understanding the Command Structure

🌟 6. Running and Verifying the Integration

⚡ Saving Configuration

⚡ Restarting Claude Desktop (Crucial Step)

⚡ Verification

⚡ Basic Interaction Test

🌟 7. Troubleshooting Common Issues

⚡ Overview

⚡ Log Files

⚡ Issue: Serena Tools Not Appearing in Claude Desktop

⚡ Issue: Tool Name Collisions

⚡ Issue: gui_log_window Problems

⚡ Issue: Permission Errors

⚡ Checking Serena GitHub Issues

🌟 8. Conclusion

⚡ Summary

⚡ Next Steps

⚡ Disclaimer

🔧 Works cited