diff --git a/app/src/agent-tools.ts b/app/src/agent-tools.ts
index 94e8a08..0d18216 100644
--- a/app/src/agent-tools.ts
+++ b/app/src/agent-tools.ts
@@ -818,7 +818,7 @@ export async function runCommand(
     if (dangerReason) throw new Error(dangerReason);
 
     const cwd = resolveSafePath(workspaceRoot, relativeCwd);
-    const wrappedCommand = applySandbox(command, { workspaceRoot, allowNetwork: network });
+    const wrappedCommand = applySandbox(command, { workspaceRoot, allowNetwork: network, cwd });
     const settings = settingsStore.getSettings();
     let stopMonitor = () => {};
     try {
@@ -913,7 +913,7 @@ export function startBackgroundCommand(
     }
 
     const cwd = resolveSafePath(workspaceRoot, relativeCwd);
-    const wrappedCommand = applySandbox(command, { workspaceRoot, allowNetwork: network });
+    const wrappedCommand = applySandbox(command, { workspaceRoot, allowNetwork: network, cwd });
     // detached so the shell becomes its own process group leader — lets
     // killProcessTree() below signal the whole group (shell + whatever it
     // spawned, e.g. `npm run dev` spawning `node`) instead of just the shell
diff --git a/app/src/command-sandbox.test.ts b/app/src/command-sandbox.test.ts
index 1a1a8de..f4b8371 100644
--- a/app/src/command-sandbox.test.ts
+++ b/app/src/command-sandbox.test.ts
@@ -79,6 +79,29 @@ describe("wrapCommand", () => {
         expect(wrapped?.args[1]).toContain("(allow network*)");
         expect(wrapped?.args[1]).not.toContain("(deny network*)");
     });
+
+    // --chdir takes precedence over the working directory bwrap inherits from
+    // the spawning process, so pinning it to the workspace root silently
+    // overrode the subdirectory the caller had already resolved.
+    it("chdirs to the requested subdirectory, not just the workspace root", () => {
+        const wrapped = wrapCommand(
+            "npm test",
+            { workspaceRoot: "/home/user/project", allowNetwork: false, cwd: "/home/user/project/packages/api" },
+            "linux",
+            has(["bwrap"])
+        );
+        const chdirIndex = wrapped!.args.indexOf("--chdir");
+        expect(chdirIndex).toBeGreaterThan(-1);
+        expect(wrapped!.args[chdirIndex + 1]).toBe("/home/user/project/packages/api");
+        // The workspace root is still what gets bound writable.
+        expect(wrapped!.args).toEqual(expect.arrayContaining(["--bind", "/home/user/project", "/home/user/project"]));
+    });
+
+    it("falls back to the workspace root when no cwd is given", () => {
+        const wrapped = wrapCommand("npm test", { workspaceRoot: "/home/user/project", allowNetwork: false }, "linux", has(["bwrap"]));
+        const chdirIndex = wrapped!.args.indexOf("--chdir");
+        expect(wrapped!.args[chdirIndex + 1]).toBe("/home/user/project");
+    });
 });
 
 describe("applySandbox", () => {
diff --git a/app/src/command-sandbox.ts b/app/src/command-sandbox.ts
index e604ca2..79d2543 100644
--- a/app/src/command-sandbox.ts
+++ b/app/src/command-sandbox.ts
@@ -73,6 +73,14 @@ export function detectSandboxCapabilities(
 export interface WrapCommandOptions {
     workspaceRoot: string;
     allowNetwork: boolean;
+    // Directory the command should start in. Defaults to the workspace root.
+    // bubblewrap is passed --chdir, which takes precedence over the working
+    // directory inherited from the spawning process, so a caller that resolved
+    // a subdirectory has to pass it through here — setting it only on the
+    // spawn options would be silently overridden. Callers are responsible for
+    // confining this to the workspace (they go through resolveSafePath); it is
+    // not re-validated here.
+    cwd?: string;
 }
 
 export interface WrappedCommand {
@@ -92,6 +100,7 @@ export function wrapCommand(
 ): WrappedCommand | null {
     const caps = detectSandboxCapabilities(platform, hasCommand);
     const root = path.resolve(opts.workspaceRoot);
+    const startDir = opts.cwd ? path.resolve(opts.cwd) : root;
 
     if (caps.mechanism === "bubblewrap") {
         const args = [
@@ -113,7 +122,7 @@ export function wrapCommand(
             root,
             root,
             "--chdir",
-            root,
+            startDir,
             "--die-with-parent",
             "--unshare-all",
         ];
diff --git a/app/src/terminal-manager.ts b/app/src/terminal-manager.ts
index 74abc12..e78c19d 100644
--- a/app/src/terminal-manager.ts
+++ b/app/src/terminal-manager.ts
@@ -59,7 +59,7 @@ export function createTerminal(
     // ordinary shell use (curl, ping, package managers) confusingly fail.
     // Filesystem confinement to the workspace still applies where the
     // platform supports it.
-    const wrapped = wrapCommand(shell, { workspaceRoot, allowNetwork: true });
+    const wrapped = wrapCommand(shell, { workspaceRoot, allowNetwork: true, cwd });
     const ptyOptions = { name: "xterm-256color", cols: 80, rows: 24, cwd, env: process.env };
     const ptyProcess = wrapped ? pty.spawn(wrapped.command, wrapped.args, ptyOptions) : pty.spawn(shell, [], ptyOptions);