Gemini CLI: tool "always" approval not persisting across terminal sessions?

Question

Using the Google Gemini CLI (google-gemini/gemini-cli, July 2025) on Pop!_OS Linux with the fish shell, I select "always" at tool approval prompts (e.g. run_shell_command, write_file, showing Approve? (y/n/always)), but every new terminal session asks for approval again. ~/.gemini/settings.json has no persistence option and the docs are silent. How do I make tool permissions persist across sessions, or is there a supported workaround?

Originally asked on GitHub: https://github.com/google-gemini/gemini-cli/issues/4340

AgentArmorHQ team · Accepted Answer

The issue was closed as **NOT_PLANNED**, and a contributor flagged it as a duplicate of a broader permissions issue (#2417). The thread does not confirm any implemented setting for persisting tool approvals; the reported behavior is that choosing `always` at a prompt (e.g. `Approve? (y/n/always)`) only applies for that terminal session, and a new session prompts again. The reporter also found no related option in `~/.gemini/settings.json` or in the repository docs (GEMINI.md, README.md, docs/cli/configuration.md, docs/troubleshooting.md, docs/sandbox.md, docs/index.md).

The only workaround mentioned is launching the CLI with the `gemini -yolo` flag, which skips all approval prompts for that session. It is all-or-nothing, and commenters expressed safety concerns; one commenter called it "a fast track to rm -rf /".

Two community proposals were made for per-tool control, but the thread does not confirm either is implemented:

- A `permissions` block in `.gemini/settings.json` with an `allowed_tools` list of tool names (e.g. `view`, `ls`, `grep`, `edit`).
- A `toolPermissions` section in `settings.json` with `alwaysAllow`, `alwaysDeny`, and `alwaysAsk` arrays; the proposal also suggested that `alwaysDeny` should remain effective even in YOLO mode.

Security note: `gemini -yolo` disables every confirmation, including for destructive commands, so it is not a substitute for per-tool allow/deny control.

AgentArmorHQ team · Answer

**What a GitHub user tried on GitHub** (Didn't work)

The reporter searched `~/.gemini/settings.json` and the repository documentation (GEMINI.md, README.md, docs/cli/configuration.md, docs/troubleshooting.md, docs/sandbox.md, docs/index.md) for a persistence setting and found none.

Source: https://github.com/google-gemini/gemini-cli/issues/4340

AgentArmorHQ team · Answer

**What @SkybuckFlying tried on GitHub** (Outcome unclear)

A commenter mentioned a startup YOLO mode flag, `gemini -yolo`, that bypasses approval prompts, but said they keep forgetting it and have not actually used it.

Source: https://github.com/google-gemini/gemini-cli/issues/4340#issuecomment-3081807122

AgentArmorHQ team · Answer

**What @quocvu tried on GitHub** (Outcome unclear)

A commenter proposed adding a `permissions` block with an `allowed_tools` list to `.gemini/settings.json`; this was a suggestion and was not tested in the thread.

Source: https://github.com/google-gemini/gemini-cli/issues/4340#issuecomment-3153782927

AgentArmorHQ team · Answer

**What @riteshsinglagoogle tried on GitHub** (Outcome unclear)

A commenter proposed a new `toolPermissions` section in `settings.json` with `alwaysAllow`, `alwaysDeny`, and `alwaysAsk` arrays; this was a design proposal only and was not confirmed as implemented.

Source: https://github.com/google-gemini/gemini-cli/issues/4340#issuecomment-3173395850

Gemini CLI: tool "always" approval not persisting across terminal sessions?

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Gemini CLI: tool "always" approval not persisting across terminal sessions?

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