To keep Claude Code away from private Obsidian notes, run it from a separate folder outside your vault and do not grant the vault as an additional directory. If a task needs notes, use a separate copy rather than the live vault. Keep edit and command approvals enabled, review the tools and directories the session can access, and maintain a backup: access controls reduce risk, while version history and backups help recover after a change.
Can Claude Code read my Obsidian vault?
It can read files that its active permissions, working-directory scope, and enabled tools allow it to reach. Anthropic’s CLI reference documents directory options and tool permissions; its security documentation describes the working-directory boundary for built-in file operations in Manual mode and notes that adding directories expands access.
That boundary is not proof that every route is restricted in the same way. Shell commands, MCP servers, plugins, hooks, and other integrations may introduce additional access or write paths. The effective setup depends on the Claude Code version, active permission mode, settings, and enabled integrations. Review the configuration for the session you are about to run rather than assuming all sessions behave alike.
Set up Claude Code so it does not use the live vault
- Start outside the vault. Open a terminal in the project folder Claude Code needs, not in the Obsidian vault. If the task does not need note contents, do not add the vault with
--add-diror an equivalent persistent additional-directory setting. Anthropic says--add-dirgrants read and edit access to additional working directories. See the CLI reference. - Keep approval prompts enabled. Use the normal or Manual permission mode and review prompts for file edits and commands with side effects. Do not use
--dangerously-skip-permissionsin a session that can reach private notes: Anthropic describes it as skipping permission prompts and equates it withbypassPermissionsin the CLI reference. - Grant only the tools the task needs. Review allow and deny rules, including
--allowedToolsand--disallowedTools, and avoid broad grants. A deny rule is not a complete boundary if shell access or extensions provide another route to the files. Review the security documentation alongside the CLI reference. - If notes are required, use a disposable copy. Copy the vault to a separate location and point the task at that copy. Keep the live vault out of the working directory and additional directories. This is a cautious workflow based on documented scope and permissions, not a guarantee that every enabled shell command or MCP integration is contained.
- Check the complete access path. Review the active working directory and added directories, permission mode, tool grants, and any MCP servers, plugins, hooks, or integrations. Obsidian URI, for example, has a
newaction and anoverwriteparameter; integrations can write into a vault independently of Claude Code’s built-in editor tool. See Obsidian URI.
Keep recovery separate from prevention
Permission settings and isolation aim to reduce access and unwanted edits. They do not replace a backup, and a backup does not prevent software from reading local files. Obsidian says Sync does not encrypt the local vault and recommends keeping a full vault backup on the primary device. Its documented simple backup methods are copying the vault folder or creating a zip file. See Obsidian’s security and privacy guidance.
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- Read Before You Buy — No Video Output: These adapters support charging and USB 2.0 data transfer, but cannot transmit video signals. Except for standard USB webcams (which use USB data only), they are not compatible with HDMI/DisplayPort cables, video-capable USB-C hubs, or docking stations with video output.
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Sync’s end-to-end encryption option applies to the remote vault; it should not be confused with a local access restriction. Keep an independent backup in a separate location, and periodically check that it can be restored. An external drive is one possible place to store a separate copy, but no particular storage product is required.
Restore an Obsidian note after an accidental change
Use Obsidian Sync version history
If Sync is enabled, open the note’s version history and restore the version you need. Obsidian’s official documentation says note-history retention depends on the plan: Standard retains note versions for one month and Plus for twelve months. Older attachment versions are kept for two weeks. These are the retention terms stated in Obsidian’s documentation accessed on October 4, 2026; check the current Version history page and your plan, since terms can change.
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Restore a deleted file or use a separate backup
Obsidian Sync’s version-history documentation also describes restoring deleted files. If Sync history does not contain the needed version, restore the file from your independent backup, taking care not to replace newer work unintentionally. Sync history is a recovery option, not a substitute for a full vault backup.
Independent reader supportYour contribution helps us test, update, and keep practical guides available for everyone.Choose safeguards by what they do
| Safeguard | Primary purpose | Important limit |
|---|---|---|
| Working-directory scope and permission settings | Reduce which files Claude Code’s built-in operations can access or change. | Coverage depends on mode and configuration; do not assume shell commands and integrations follow the same boundary. |
| Separate project folder or disposable vault copy | Keep work away from the live vault. | Review shell and MCP access as well; a copy is risk reduction, not a universal guarantee. |
| Obsidian Sync version history | Recover older note versions or deleted files within the applicable retention window. | Retention is plan dependent and Sync does not encrypt the local vault. |
| Independent full-vault backup | Recover the vault if local files are damaged or history is unavailable. | It does not prevent access; keep it separate and verify that restoration works. |
Anthropic’s configuration details and Obsidian Sync terms may change. Check the official documentation linked above against the Claude Code version, settings, and Sync plan you actually use.
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