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To reduce the chance that Claude Code can read or change private Obsidian notes, run it from a project folder outside your vault, do not add the vault as an accessible directory, keep permission prompts enabled, and avoid bypass-permissions mode. If a task needs note files, use a separate copy of the vault. These steps reduce risk; they are not a guarantee that every shell command, MCP server, or other integration is isolated. Keep an independent backup for recovery.
Can Claude Code read my Obsidian vault?
It can read files that are within the access available to the active Claude Code session. The exact boundary depends on the session’s working directory, added directories, permissions, settings, and enabled tools. Anthropic documents a working-directory boundary for built-in file operations in Manual mode, and says additional directories expand access. That boundary should not be treated as proof that every shell command, MCP server, hook, plugin, or integration is equally constrained. Review the effective settings for your installed version rather than assuming all sessions behave alike. See the Claude Code CLI reference and Anthropic security documentation.
Set up Claude Code so it does not need the live vault
For work that does not need note contents
- Start in a separate project folder. Open a terminal in the project Claude Code needs to work on, not in the Obsidian vault or one of its subfolders.
- Do not grant the vault as an additional directory. Avoid
--add-dirand equivalent persistent additional-directory settings for the live vault. The CLI reference says--add-dirgrants read and edit access to additional working directories. - Use normal or Manual permissions. Keep approval prompts for file edits and side-effecting commands so you can review actions before they run.
- Do not use bypass permissions for a session that can reach private notes. The CLI describes
--dangerously-skip-permissionsas skipping permission prompts and equates it withbypassPermissions.
This separate-folder workflow is a cautious recommendation based on documented directory scope and permission controls, not a vendor-certified guarantee. It is most useful when the task can be completed without note contents.
For work that needs note files
- Make a separate copy of the vault, or copy only the notes the task needs into a disposable working folder.
- Point Claude Code at that copy, and keep the live vault outside both its working directory and any additional directories you grant.
- Review permission modes and tool rules before starting. The CLI documents
--allowedToolsand--disallowedTools; avoid broad grants and consider which tools actually need to be available. - Discard or carefully review the working copy after the task. Apply desired changes to the live vault yourself rather than letting an agent experiment on the only copy.
A copy limits the consequences of mistaken edits to that copy, but it is still a risk-reduction measure, particularly if Bash or MCP tools are enabled. For current controls and configuration details, consult the CLI reference and security documentation.
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Review access beyond Claude Code’s built-in file tools
Do not assess exposure by looking only at the built-in editor or file tools. Shell commands, MCP servers, plugins, hooks, and other enabled integrations may provide additional routes to files or services. A deny rule for one tool is only one part of the setup; check which tools are enabled and what directories or capabilities they can reach. Obsidian integrations deserve attention too: Obsidian URI supports a new action and an overwrite parameter, so another application or automation can write into a vault. See the Obsidian URI documentation.
Keep a backup for recovery
Access controls reduce the chance of unwanted reading or edits; they do not restore a damaged file. Obsidian recommends making a full backup on the primary device. Its documented simple methods include copying the vault folder or creating a ZIP archive. Keep a backup in a separate location, and periodically confirm you can restore it. A portable external drive is one possible place to store a separate copy, but no particular product is required.
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Obsidian Sync can also help restore earlier note versions and deleted files. The official version-history page lists retention of one month for notes on Standard and twelve months on Plus; older attachment versions are kept for two weeks. These terms can change, so check the current plan details and your account’s available history before relying on a particular recovery window. Sync is a recovery option, not a local access boundary: Obsidian says the local vault is not encrypted by Sync. Its end-to-end encryption option applies to the remote vault, not to local files. See Obsidian Sync version history and Obsidian Sync security and privacy.
Independent reader supportYour contribution helps us test, update, and keep practical guides available for everyone.Restore an Obsidian note after an accidental change
If you use Obsidian Sync
- Open the affected note in Obsidian.
- Open the note’s version history and choose an earlier version to review or restore, following the current controls in Obsidian’s version-history guide.
- If the note was deleted, use Sync’s deleted-file restoration option while the file remains available in its recovery history.
For a lost attachment or a version outside the stated history window, check your independent backup. Sync’s retention for older attachment versions is shorter than its note-version retention.
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If you do not use Sync
Restore the note or vault from your independent backup, using the copy or archive you made before the incident. If you have no backup or version history, the official documentation cited here does not establish another guaranteed way to recover the overwritten contents.
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Choose controls by what they do
| Control | Primary purpose | What it does not establish |
|---|---|---|
| Separate working directory; do not add the vault | Reduce the files Claude Code is intended to access | That every shell command, MCP server, or integration is equally constrained |
| Permission prompts and tool rules | Review or limit tool actions and edits | That a single deny rule covers every route to files |
| Disposable vault copy | Keep experiments away from the live notes | That the copy itself is inaccessible to enabled tools |
| Obsidian Sync version history | Recover eligible older note versions or deleted files | Prevent local software from reading the vault |
| Independent vault backup | Restore from a separate copy if needed | Prevent access or edits in the live vault |
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