diff --git a/src/agent/cli/commands/run.ts b/src/agent/cli/commands/run.ts
index e404013b4..df7127ab2 100644
--- a/src/agent/cli/commands/run.ts
+++ b/src/agent/cli/commands/run.ts
@@ -7,6 +7,7 @@
  */
 
 import { Agent } from "../../runner.js";
+import type { AgentOptions } from "../../types.js";
 import type { ToolsConfig } from "../../tools/policy.js";
 import { cyan, yellow, dim } from "../colors.js";
 
@@ -198,7 +199,7 @@ export async function runCommand(args: string[]): Promise<void> {
     baseUrl: opts.baseUrl,
     systemPrompt: opts.system,
     thinkingLevel: opts.thinking as any,
-    reasoningMode: (opts.reasoning as any) ?? undefined,
+    reasoningMode: opts.reasoning as AgentOptions["reasoningMode"],
     cwd: opts.cwd,
     sessionId: opts.session,
     debug: opts.debug,
diff --git a/src/agent/cli/interactive.ts b/src/agent/cli/interactive.ts
index bd6131aba..3a4e36591 100644
--- a/src/agent/cli/interactive.ts
+++ b/src/agent/cli/interactive.ts
@@ -349,7 +349,7 @@ class InteractiveCLI {
       model: this.opts.model,
       systemPrompt: this.opts.system,
       thinkingLevel: this.opts.thinking as AgentOptions["thinkingLevel"],
-      reasoningMode: (this.opts.reasoning as AgentOptions["reasoningMode"]) ?? undefined,
+      reasoningMode: this.opts.reasoning as AgentOptions["reasoningMode"],
       cwd: this.opts.cwd,
       sessionId,
     });
diff --git a/src/agent/cli/non-interactive.ts b/src/agent/cli/non-interactive.ts
index 004facfc5..2cff5c4f0 100644
--- a/src/agent/cli/non-interactive.ts
+++ b/src/agent/cli/non-interactive.ts
@@ -177,7 +177,7 @@ async function main() {
     baseUrl: opts.baseUrl,
     systemPrompt: opts.system,
     thinkingLevel: opts.thinking as any,
-    reasoningMode: (opts.reasoning as any) ?? undefined,
+    reasoningMode: opts.reasoning as any,
     cwd: opts.cwd,
     sessionId: opts.session,
     debug: opts.debug,
diff --git a/src/agent/cli/output.ts b/src/agent/cli/output.ts
index b47468aca..fe4fa058a 100644
--- a/src/agent/cli/output.ts
+++ b/src/agent/cli/output.ts
@@ -249,8 +249,8 @@ export function createAgentOutput(params: {
           state.streaming = false;
           state.lastAssistantText = text;
 
-          // Extract and store thinking content
-          const thinking = extractThinking(msg);
+          // Extract and store thinking content (skip when off)
+          const thinking = reasoningMode !== "off" ? extractThinking(msg) : "";
           state.lastAssistantThinking = thinking;
 
           // Show thinking at end for "on" mode
diff --git a/src/agent/runner.ts b/src/agent/runner.ts
index c395e3952..4440f2376 100644
--- a/src/agent/runner.ts
+++ b/src/agent/runner.ts
@@ -70,7 +70,7 @@ export class Agent {
   private readonly skillManager?: SkillManager;
   private readonly contextWindowGuard: ContextWindowGuardResult;
   private readonly debug: boolean;
-  private readonly reasoningMode: ReasoningMode;
+  private reasoningMode: ReasoningMode;
   private toolsOptions: AgentOptions;
   private readonly originalToolsConfig?: ToolsConfig;
   private readonly stderr: NodeJS.WritableStream;
@@ -267,6 +267,18 @@ export class Agent {
       this.agent.setThinkingLevel(options.thinkingLevel);
     }
 
+    // Resolve reasoningMode: options > profile config > storedMeta > default "stream"
+    if (!options.reasoningMode) {
+      const profileReasoningMode = this.profile?.getProfile()?.config?.reasoningMode;
+      const metaReasoningMode = storedMeta?.reasoningMode as ReasoningMode | undefined;
+      const resolved = profileReasoningMode ?? metaReasoningMode ?? "stream";
+      if (resolved !== this.reasoningMode) {
+        this.reasoningMode = resolved;
+        // Re-create output with correct reasoningMode
+        this.output = createAgentOutput({ stdout, stderr: this.stderr, reasoningMode: this.reasoningMode });
+      }
+    }
+
     this.agent.setModel(model);
 
     // Save original tools config from options (for later merging during reload)