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Put allow and deny rules in the correct settings.json, remember that deny rules win, and inspect the effective result with /permissions. Never commit API keys or passwords: inject credentials at runtime through environment variables or secure credential storage, including ${API_KEY} expansion in MCP configuration.
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Choose a permission mode before you start
Claude Code does not have one all-or-nothing security switch. Its permission mode determines how much work can proceed without an interactive approval. Begin with the mode that gives you the smallest useful blast radius, then add individual rules as the workflow proves it needs them.
| Mode | What it does | Best use | Main risk |
|---|---|---|---|
default |
Keeps approval prompts for operations that need them. | Routine development when you want to review commands, tests, and edits. | Prompts can become repetitive, encouraging users to approve without reading. |
plan |
Analysis-only operation with a proposed plan; it does not make edits or execute commands. | Understanding an unfamiliar repository, scoping a change, or reviewing a proposed approach. | You cannot validate a fix by running it until you leave plan mode. |
acceptEdits |
Batches approval for file edits during the session while other operations retain their normal controls. | A focused editing session in a trusted checkout where repeated edit prompts slow work. | A mistaken instruction can authorize several file changes in one session. |
bypassPermissions |
Skips permission prompts. | Only a deliberately controlled, isolated environment with separate safeguards. | A prompt, script, or generated command can act without the approval boundary. |
For a no-change review, start Claude Code with:
claude --permission-mode planUse default as the normal baseline. Treat acceptEdits as a temporary convenience, not a permanent project policy. The command-line option commonly associated with bypassing prompts is --dangerously-skip-permissions; its name is an accurate warning. Avoid it for ordinary development.
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Understand what Claude Code can access by default
Read-only inspection is the default behavior. Claude Code can inspect the project and, where needed, read libraries and dependencies outside the working directory. Shell commands, tests, and edits require approval unless a rule or selected mode changes that behavior.
Write access is narrower than read access: writes are confined to the directory where Claude Code started and its descendants unless you explicitly grant broader access. Start it at the repository root, or at a deliberately isolated checkout, rather than at a broad home directory. This choice establishes the default write boundary before you add any policy rules.
What the startup boundary means in practice
- Starting in
~/work/projectpermits writes in that directory and its subdirectories, subject to permission prompts and rules. - A sibling directory such as
~/work/shared-libis not automatically part of the write scope. - Reading an external dependency does not automatically authorize modifying it.
- A command that reaches outside the repository can still have effects beyond the intended project if you approve it; review the exact command, not only the filename it mentions.
Build a least-privilege policy in settings.json
Use project settings for rules that should travel with a repository, and local settings for developer-specific exceptions. The documented rule form is Tool(optional-specifier). A tool name alone applies broadly; a specifier narrows the match to a command or path pattern.
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{
"permissions": {
"allow": [
"Bash(git diff:*)",
"Bash(git status:*)",
"Bash(npm test:*)",
"Edit(docs/**)"
],
"deny": [
"Bash(rm -rf:*)",
"Bash(curl:*)",
"Bash(wget:*)",
"Edit(.env*)",
"Edit(**/secrets/**)"
]
}
}Keep patterns as narrow as the task allows. For example, Bash(git diff:*) is materially safer than allowing every shell command, and Edit(docs/**) does not authorize edits to application code or configuration. Do not treat this example as a universal allowlist: command names, test runners, and sensitive paths differ by repository.
Deny rules override allow rules
If a request matches both an allow rule and a deny rule, the deny wins. Use that precedence to create a safety net around broad workflow allowances. For instance, a project may permit a test command while denying a path that contains production credentials. Place sensitive-file and destructive-command denials deliberately, then test them rather than assuming the pattern matched.
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Review the effective policy
Rules can come from several levels and from command-line choices. In an active session, run:
/permissionsReview the resulting allow and deny entries, their source, and the operations they cover. This catches a common failure mode: editing one settings file while a higher-precedence file or command-line argument continues to govern the session.
Know which settings file wins
Claude Code applies policy in this order, from highest to lowest precedence:
- Enterprise managed policy.
- Command-line arguments.
- Local project settings in
.claude/settings.local.json. - Shared project settings in
.claude/settings.json. - User settings in
~/.claude/settings.json.
A lower-level file cannot weaken a higher-level restriction. This makes the arrangement useful for teams: developers can keep personal preferences in user settings, repositories can distribute reviewed defaults, and the organization can enforce non-overridable controls above both.
Enterprise managed-settings.json locations
Managed policy files are installed at these documented locations:
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/etc/claude-code/managed-settings.json
Use managed settings for controls that must not be bypassed by a project or individual developer. Keep the file owned and distributed by the team responsible for endpoint policy, and review changes through the organization’s normal change-control process.
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Shared versus local project settings
Commit .claude/settings.json when the rules are part of the repository’s expected workflow and have been reviewed. Keep .claude/settings.local.json uncommitted for machine-specific paths or temporary exceptions. Never use a local file as a place to hide a secret; local does not mean encrypted, and it can still be copied, backed up, or exposed.
Expand the sandbox only when the workflow requires it
The default startup boundary is intentionally small. If a build genuinely needs a sibling library or another working tree, add only that directory:
claude --add-dir ../shared-libUse one --add-dir path for each required location, and verify that the path is trusted before granting it. Do not add a home directory, a filesystem root, a downloads folder, or a directory that contains unrelated credentials simply to avoid a missing-file error.
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- Identify the exact file or command that failed because it is outside the startup directory.
- Confirm that the workflow truly needs that location rather than a copy or generated artifact inside the repository.
- Check who can modify the added directory and whether it contains secrets or untrusted files.
- Add the narrowest directory that satisfies the dependency.
- Run
/permissionsand review the resulting scope before continuing.
Remove the extra directory from later sessions when it is no longer needed. A temporary expansion should not become a permanent, invisible trust assumption.
Use a devcontainer or VM for hostile or high-impact work
Permission prompts reduce accidental actions, but they are not a complete isolation boundary. Prompts, scripts, generated files, and web content can contain instructions intended to manipulate an agent or a developer. When the input is untrusted, or when a mistake could affect production credentials or the host operating system, put Claude Code inside a devcontainer or virtual machine.
When a stronger boundary is justified
- You are analyzing a repository downloaded from an unknown source.
- Build scripts execute installers, code generators, or arbitrary post-install hooks.
- The task involves web content, issue text, or documents that may contain hostile instructions.
- The checkout has access to production-like credentials, deployment tools, or sensitive data.
- You need to experiment with
bypassPermissionsfor a controlled automation job.
Layered isolation
Use several controls together: an isolated checkout, a narrowly scoped startup directory, default approval prompts, restricted network access where practical, and a devcontainer or VM for untrusted work. A container or VM limits host impact, but it does not make secrets safe if you mount them into the environment or print them in logs. Isolation and secret handling must be designed together.
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Protect API keys, proxy credentials, and MCP secrets
Do not hard-code passwords, API keys, proxy tokens, or MCP credentials in committed scripts, project settings, prompts, or documentation. A permission policy can restrict what Claude Code does, but it cannot make a literal secret safe after that secret has been committed, copied into a tool output, or printed to a log.
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Inject credentials at runtime
Use secure credential storage supported by your operating environment, or export a variable for the session that needs it. In MCP configuration, environment-variable expansion is supported in command, args, env, url, and headers. A committed template can therefore reference a variable without containing its value:
{
"mcpServers": {
"internal-api": {
"url": "https://api.example.invalid/mcp",
"headers": {
"Authorization": "Bearer ${API_KEY}"
}
}
}
}The hostname above is an example placeholder, not a service recommendation. In your own configuration, keep the real endpoint and token outside version control, set API_KEY through an approved secret mechanism, and ensure shell history, CI logs, and diagnostic output do not echo it.
Keep secret-bearing files out of edit scope
Add explicit deny rules for common secret locations such as .env files, credential directories, private keys, and deployment configuration. Match the repository’s actual layout; a generic pattern that misses a differently named file provides false confidence. Also deny commands whose purpose is to print or upload files when the command pattern can be narrowed safely.
Rotate after an exposure
If a key appears in a prompt, tool output, commit, log, or generated artifact, treat it as compromised. Revoke or rotate it through the issuing service, remove the exposed copy from the repository and accessible logs where possible, and inspect related credentials. Changing a permission rule does not invalidate a key that has already leaked.
Configure a team policy without blocking useful work
A team policy should define the minimum access needed by the repository rather than copying one developer’s preferences. Start with a shared .claude/settings.json that allows safe, repeatable inspection and build commands. Add denies for destructive operations and sensitive paths. Enforce organization-wide restrictions in managed settings, then let project settings add narrower allowances that do not conflict with those restrictions.
Suggested rollout
- Begin in
planmode and document the commands and directories the workflow actually needs. - Run in
defaultmode and record repeated approval prompts. - Convert only predictable, low-risk prompts into narrowly scoped allow rules.
- Add deny rules for destructive commands, network fetches that are not required, and secret-bearing paths.
- Review
/permissionson a clean checkout and test both an allowed operation and an intentionally denied one. - Commit the reviewed project settings and enforce non-overridable requirements through managed policy.
Review policy changes as code. A new allow rule can enlarge the blast radius even when the change looks like a convenience tweak.
Troubleshoot common permission and sandbox problems
Claude Code keeps asking for the same command
Check whether the command varies by arguments, working directory, or shell wrapper. A rule for Bash(git diff:*) will not necessarily match a different command that performs a similar operation. Use the narrowest stable pattern, then confirm the effective match in /permissions. Do not solve repetitive prompts by switching to bypassPermissions.
An allow rule appears to be ignored
Look for a matching deny rule, because deny takes precedence. Then inspect higher-precedence policy: managed settings, command-line arguments, and local project settings can all change the result. Check spelling, path globbing, and whether the request is using a different tool name than the one in the rule.
A required file is outside the write boundary
First ask whether the file can be copied or generated inside the repository. If not, restart with a specific trusted directory using --add-dir, and review the expanded scope. Do not grant a broad parent directory merely because one dependency is missing.
A command runs but cannot reach a service
Separate permission from connectivity. An allowed command may still be blocked by the container, VM, firewall, proxy, or missing runtime credential. Verify that the required environment variable is present without printing its value, and check the MCP configuration for correct variable expansion in the field where it is used.
A secret was printed or committed
Stop using the credential, rotate or revoke it, and remove it from future outputs and commits. Search logs and generated files for additional copies. Add a deny rule for the affected path or command, then test the rule in a fresh session. The policy change is preventive; rotation is the immediate response.
Quick Recap
Audit checklist before normal work
- Claude Code starts in the repository root or an intentionally isolated checkout.
- The session uses
defaultunless analysis-onlyplanmode is the deliberate choice. - No routine workflow depends on
--dangerously-skip-permissions. - Every
--add-dirpath is necessary, trusted, and as narrow as possible. - Allow rules specify exact command or path patterns instead of whole-tool access where feasible.
- Deny rules cover destructive commands and secret-bearing paths, and their precedence has been tested.
/permissionsshows the policy you intended after all settings layers are applied.- Project settings contain no literal API keys, passwords, private keys, or proxy tokens.
- MCP credentials use runtime variables such as
${API_KEY}or an approved secure store. - Untrusted repositories and high-impact operations run inside a devcontainer or VM.
- Team-wide restrictions live in managed settings when developers must not override them.
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