[BUG] alwaysThinkingEnabled setting not respected since v2.0.64

[andrewklingelhofer]

Preflight Checklist

• I have searched existing issues and this hasn't been reported yet
• This is a single bug report (please file separate reports for different bugs)
• I am using the latest version of Claude Code

What's Wrong?

The alwaysThinkingEnabled setting in ~/.claude/settings.json is no longer being respected. Thinking mode defaults to OFF on every new session, even though the setting is configured to true.

This is a regression - the setting was working correctly in previous versions.

What Should Happen?

When alwaysThinkingEnabled: true is set in ~/.claude/settings.json, Claude Code should start with thinking mode enabled by default (as indicated by "Thinking on (tab to toggle)" in the status line).

Error Messages/Logs

No errors - the setting is silently ignored.

Steps to Reproduce

1. Add "alwaysThinkingEnabled": true to ~/.claude/settings.json:

   {
     "alwaysThinkingEnabled": true
   }

2. Start a new Claude Code session
3. Observe the status line shows thinking mode is OFF
4. Have to manually press Tab to enable thinking mode

Claude Model

Opus 4.5 (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

Versions prior to 2.0.64

Claude Code Version

2.0.64

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Ghostty

Additional Information

Related issue: #10623 discusses alwaysThinkingEnabled but conflates multiple different issues. This bug report is specifically about the setting not being respected on startup - a clear regression in v2.0.64.

[github-actions]

Found 2 possible duplicate issues:

1. [BUG] Settings not applied: alwaysThinkingEnabled ignored and inconsistent permission behavior #10623
2. Model setting in settings.json is ignored on startup - defaults to Sonnet instead of configured Opus #13242

This issue will be automatically closed as a duplicate in 3 days.

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🤖 Generated with Claude Code

[damien-king]

I have the opposite problem, CC always opens with thinking mode on, regardless of the settings.json, toggling with TAB changes the setting in the file but ultimately it's ignored resulting in thinking ON again after I restart CC.

[Elijas]

It's actually not respected since 2.0.62
2.0.61 still respects it

[milobird]

I'm experiencing the same since 2.0.62.

[Elijas]

how do you prevent from autoupdate?

export DISABLE_AUTOUPDATER=1
doesnt seem to work

[segevfiner]

I'm on 2.0.65, and thinking seems to be enabled by default, and Claude Code itself tells me to go and report a bug in GitHub so there we are...