diff --git a/packages/server/src/server/agent/providers/claude/agent.ts b/packages/server/src/server/agent/providers/claude/agent.ts
index 62813bcec..7761d8ea0 100644
--- a/packages/server/src/server/agent/providers/claude/agent.ts
+++ b/packages/server/src/server/agent/providers/claude/agent.ts
@@ -1,3 +1,4 @@
+import type { ChildProcess } from "node:child_process";
 import { randomUUID } from "node:crypto";
 import fs from "node:fs";
 import { promises } from "node:fs";
@@ -96,6 +97,7 @@ import {
   type ResolvedProviderLaunch,
 } from "../../provider-launch-config.js";
 import { withTimeout } from "../../../../utils/promise-timeout.js";
+import { terminateWithTreeKill } from "../../../../utils/tree-kill.js";
 import { execCommand } from "../../../../utils/spawn.js";
 import { composeSystemPromptParts } from "../../system-prompt.js";
 
@@ -1880,6 +1882,7 @@ class ClaudeAgentSession implements AgentSession {
   private readonly queryFactory?: ClaudeQueryFactory;
   private readonly resolveBinary: () => Promise<string>;
   private query: Query | null = null;
+  private childProcess: ChildProcess | null = null;
   private input: AsyncMessageInput<SDKUserMessage> | null = null;
   private claudeSessionId: string | null;
   private persistence: AgentPersistenceHandle | null;
@@ -2353,6 +2356,22 @@ class ClaudeAgentSession implements AgentSession {
     await this.awaitWithTimeout(this.query?.return?.(), "close query return");
     this.query = null;
     this.input = null;
+    // Terminate the entire process tree (claude + MCP children) to prevent
+    // orphan accumulation. The SDK's internal cleanup may only kill the
+    // direct child process.
+    if (this.childProcess) {
+      const result = await terminateWithTreeKill(this.childProcess, {
+        gracefulTimeoutMs: 2_000,
+        forceTimeoutMs: 2_000,
+      });
+      if (result === "kill-timeout") {
+        this.logger.warn(
+          { pid: this.childProcess.pid, agentId: this.agentId },
+          "Claude process tree did not report exit after SIGKILL",
+        );
+      }
+      this.childProcess = null;
+    }
     if (this.persistSession === false && this.claudeSessionId) {
       // Claude Code currently ignores --no-session-persistence outside --print mode
       // (see `claude --help`), so the SDK's persistSession=false is silently dropped
@@ -2751,6 +2770,18 @@ class ClaudeAgentSession implements AgentSession {
       } catch {
         /* ignore */
       }
+      // Tree-kill the old process tree now that the SDK has cleaned up.
+      // If we skip this, MCP children of the previous claude process can
+      // survive as orphans when the session spawns a replacement query.
+      if (this.childProcess) {
+        await terminateWithTreeKill(this.childProcess, {
+          gracefulTimeoutMs: 2_000,
+          forceTimeoutMs: 2_000,
+        }).catch(() => {
+          /* process may already be dead */
+        });
+        this.childProcess = null;
+      }
     }
 
     // Preserve claudeSessionId across query recreation so buildOptions() passes
@@ -2767,6 +2798,9 @@ class ClaudeAgentSession implements AgentSession {
         runtimeSettings: this.runtimeSettings,
         launchEnv: this.launchEnv,
         queryFactory: this.queryFactory,
+        onChildProcess: (child) => {
+          this.childProcess = child;
+        },
       },
     );
     const fastMode = this.resolveFastModeSetting();
diff --git a/packages/server/src/server/agent/providers/claude/query.ts b/packages/server/src/server/agent/providers/claude/query.ts
index a1917e400..ccd511816 100644
--- a/packages/server/src/server/agent/providers/claude/query.ts
+++ b/packages/server/src/server/agent/providers/claude/query.ts
@@ -21,6 +21,8 @@ export interface ClaudeQueryContext {
   runtimeSettings?: ProviderRuntimeSettings;
   launchEnv?: Record<string, string>;
   queryFactory?: ClaudeQueryFactory;
+  /** Called with the spawned child process so the caller can tree-kill it on close. */
+  onChildProcess?: (child: ChildProcess) => void;
 }
 
 function isChildProcessWithStreams(child: ChildProcess): child is ChildProcessWithoutNullStreams {
@@ -54,9 +56,9 @@ function resolveClaudeSpawnCommand(
 
 function applyRuntimeSettingsToClaudeOptions(
   options: ClaudeOptions,
-  runtimeSettings?: ProviderRuntimeSettings,
-  launchEnv?: Record<string, string>,
+  context: ClaudeQueryContext,
 ): ClaudeOptions {
+  const { runtimeSettings, launchEnv, onChildProcess } = context;
   return {
     ...options,
     spawnClaudeCodeProcess: (spawnOptions) => {
@@ -94,6 +96,7 @@ function applyRuntimeSettingsToClaudeOptions(
         // The command is always a resolved binary path, so shell routing is unnecessary.
         shell: false,
       });
+      onChildProcess?.(child);
       if (typeof options.stderr === "function") {
         child.stderr?.on("data", (chunk: Buffer | string) => {
           options.stderr?.(chunk.toString());
@@ -111,10 +114,6 @@ export function claudeQuery(input: ClaudeQueryInput, context: ClaudeQueryContext
   const launchQuery = context.queryFactory ?? query;
   return launchQuery({
     ...input,
-    options: applyRuntimeSettingsToClaudeOptions(
-      input.options,
-      context.runtimeSettings,
-      context.launchEnv,
-    ),
+    options: applyRuntimeSettingsToClaudeOptions(input.options, context),
   });
 }