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What carries across both versions automatically.

Because the desktop app and browser version connect to the same Claude account, most of your configuration is shared without any effort on your part.

Settings and data shared across both interfaces:

• Custom Instructions: Written once, applied in both. Changes made in either version appear in both.
• Projects: Created and edited in either interface; available in both. All conversation history within Projects is shared.
• Conversation history: All conversations are stored in your account and accessible from either interface.
• Account settings: Profile, email, subscription tier, and payment information are account-level, not interface-level.

What is specific to the desktop app.

Some settings exist only in the desktop app because they relate to your local computer environment:

• MCP server configuration: Defined in the desktop app only. MCP connections are local to your specific computer and do not sync to the browser version, which does not support MCP.
• Operating system integration: Launch-at-startup preferences, keyboard shortcuts for opening the app, and system notification settings are operating-system-level and desktop-app-specific.
• Local application preferences: Any interface preferences that are specific to your installed desktop app version.

Keeping Custom Instructions healthy across both.

Since Custom Instructions sync automatically, you can update them from whichever interface you have open at the moment. The change will appear in both.

A practical habit worth building: keep a copy of your Custom Instructions in a separate notes application outside of Claude entirely. This serves as a backup if something goes wrong with an account sync, as a reference when you want to refine your instructions thoughtfully using a text editor, and as a personal record of how your configuration evolves over time. Creating this backup takes five minutes and has saved many users frustration when their instructions were unexpectedly reset.

Project organization across both interfaces.

Projects work consistently across both the desktop app and browser version. A practical approach:

• Create new Projects from whichever interface you have open – there is no reason to switch interfaces just to create a Project
• If you use MCP in the desktop app, consider noting in the Project description which Projects involve local file access, so you remember to work on them from your desktop app
• Projects that do not require MCP work equally well in either interface

Interface-specific configuration tips.

For the desktop app:

• Configure a keyboard shortcut at the operating system level to open Claude with a single keystroke from anywhere on your computer
• Enable launch-at-startup if you use Claude throughout every workday – it will be ready without any browser step
• Explore the desktop app's settings for any current interface-specific preferences in your version

For the browser version:

• Bookmark claude.ai in your browser's bookmarks bar for single-click access
• Use your browser's tab management (pinned tabs, tab groups) to keep a Claude tab available throughout your browser session
• Consider creating a browser shortcut on your desktop that opens directly to claude.ai

Sync timing.

Custom Instructions and Project changes sync in real time across devices. If you update your Custom Instructions in the desktop app and then open the browser version seconds later, you may occasionally need to refresh the browser page to see the updated settings. This is a brief propagation delay, not a sync failure.