diff --git a/packages/coding-agent/CHANGELOG.md b/packages/coding-agent/CHANGELOG.md
index 626c61c7..8e20a044 100644
--- a/packages/coding-agent/CHANGELOG.md
+++ b/packages/coding-agent/CHANGELOG.md
@@ -24,6 +24,7 @@
 
 ### Fixed
 
+- Fixed git package installs with custom `npmCommand` values such as `pnpm` by avoiding npm-specific production flags in that compatibility path ([#3604](https://github.com/badlogic/pi-mono/issues/3604))
 - Fixed first user messages rendering without spacing after existing notices such as compaction summaries or status messages ([#3613](https://github.com/badlogic/pi-mono/issues/3613))
 - Fixed the handoff extension example to use the replacement-session context after creating a new session, avoiding stale `ctx` errors when it installs the generated prompt ([#3606](https://github.com/badlogic/pi-mono/issues/3606))
 - Fixed session replacement and `/quit` teardown ordering to run host-owned extension UI cleanup synchronously after `session_shutdown` handlers complete but before invalidating the old extension context, preventing stale extension UI from rendering against a disposed session.
diff --git a/packages/coding-agent/README.md b/packages/coding-agent/README.md
index 6ed1b438..97a4334b 100644
--- a/packages/coding-agent/README.md
+++ b/packages/coding-agent/README.md
@@ -384,7 +384,7 @@ pi update                               # skips pinned packages
 pi config                               # enable/disable extensions, skills, prompts, themes
 ```
 
-Packages install to `~/.pi/agent/git/` (git) or global npm. Use `-l` for project-local installs (`.pi/git/`, `.pi/npm/`). Git packages install dependencies with `npm install --omit=dev`, so runtime deps must be listed under `dependencies`. If you use a Node version manager and want package installs to reuse a stable npm context, set `npmCommand` in `settings.json`, for example `["mise", "exec", "node@20", "--", "npm"]`.
+Packages install to `~/.pi/agent/git/` (git) or global npm. Use `-l` for project-local installs (`.pi/git/`, `.pi/npm/`). Git packages install dependencies with `npm install --omit=dev` by default, so runtime deps must be listed under `dependencies`; when `npmCommand` is configured, git packages use plain `install` for compatibility with wrappers. If you use a Node version manager and want package installs to reuse a stable npm context, set `npmCommand` in `settings.json`, for example `["mise", "exec", "node@20", "--", "npm"]`.
 
 Create a package by adding a `pi` key to `package.json`:
 
diff --git a/packages/coding-agent/docs/extensions.md b/packages/coding-agent/docs/extensions.md
index 37d92896..bf65334d 100644
--- a/packages/coding-agent/docs/extensions.md
+++ b/packages/coding-agent/docs/extensions.md
@@ -145,7 +145,7 @@ To share extensions via npm or git as pi packages, see [packages.md](packages.md
 
 npm dependencies work too. Add a `package.json` next to your extension (or in a parent directory), run `npm install`, and imports from `node_modules/` are resolved automatically.
 
-For distributed pi packages installed with `pi install` (npm or git), runtime deps must be in `dependencies`. Package installation uses production installs (`npm install --omit=dev`), so `devDependencies` are not available at runtime.
+For distributed pi packages installed with `pi install` (npm or git), runtime deps must be in `dependencies`. Package installation uses production installs (`npm install --omit=dev`) by default, so `devDependencies` are not available at runtime; when `npmCommand` is configured, git packages use plain `install` for compatibility with wrappers.
 
 Node.js built-ins (`node:fs`, `node:path`, etc.) are also available.
 
diff --git a/packages/coding-agent/docs/settings.md b/packages/coding-agent/docs/settings.md
index d745edef..609a89ba 100644
--- a/packages/coding-agent/docs/settings.md
+++ b/packages/coding-agent/docs/settings.md
@@ -127,7 +127,7 @@ When a provider requests a retry delay longer than `maxDelayMs` (e.g., Google's
 }
 ```
 
-`npmCommand` is used for all npm package-manager operations, including `npm root -g`, installs, uninstalls, and `npm install` inside git packages. Use argv-style entries exactly as the process should be launched.
+`npmCommand` is used for all npm package-manager operations, including `npm root -g`, installs, uninstalls, and dependency installs inside git packages. Use argv-style entries exactly as the process should be launched. When `npmCommand` is configured, git package dependency installs use plain `install` to avoid npm-specific flags in wrappers or alternate package managers.
 
 ### Sessions
 
diff --git a/packages/coding-agent/src/core/package-manager.ts b/packages/coding-agent/src/core/package-manager.ts
index fded4d50..b386bf7b 100644
--- a/packages/coding-agent/src/core/package-manager.ts
+++ b/packages/coding-agent/src/core/package-manager.ts
@@ -1661,6 +1661,14 @@ export class DefaultPackageManager implements PackageManager {
 		await this.runCommand(npmCommand.command, [...npmCommand.args, ...args], options);
 	}
 
+	private getGitDependencyInstallArgs(): string[] {
+		const configuredCommand = this.settingsManager.getNpmCommand();
+		if (configuredCommand && configuredCommand.length > 0) {
+			return ["install"];
+		}
+		return ["install", "--omit=dev"];
+	}
+
 	private runNpmCommandSync(args: string[]): string {
 		const npmCommand = this.getNpmCommand();
 		return this.runCommandSync(npmCommand.command, [...npmCommand.args, ...args]);
@@ -1705,7 +1713,7 @@ export class DefaultPackageManager implements PackageManager {
 		}
 		const packageJsonPath = join(targetDir, "package.json");
 		if (existsSync(packageJsonPath)) {
-			await this.runNpmCommand(["install", "--omit=dev"], { cwd: targetDir });
+			await this.runNpmCommand(this.getGitDependencyInstallArgs(), { cwd: targetDir });
 		}
 	}
 
@@ -1740,7 +1748,7 @@ export class DefaultPackageManager implements PackageManager {
 
 		const packageJsonPath = join(targetDir, "package.json");
 		if (existsSync(packageJsonPath)) {
-			await this.runNpmCommand(["install", "--omit=dev"], { cwd: targetDir });
+			await this.runNpmCommand(this.getGitDependencyInstallArgs(), { cwd: targetDir });
 		}
 	}
 
diff --git a/packages/coding-agent/test/package-manager.test.ts b/packages/coding-agent/test/package-manager.test.ts
index 3d0e9358..f116cc74 100644
--- a/packages/coding-agent/test/package-manager.test.ts
+++ b/packages/coding-agent/test/package-manager.test.ts
@@ -500,6 +500,33 @@ Content`,
 			expect(runCommandSpy).toHaveBeenCalledWith("npm", ["install", "--omit=dev"], { cwd: targetDir });
 		});
 
+		it("should use plain install for git package dependencies when npmCommand is configured", async () => {
+			settingsManager = SettingsManager.inMemory({
+				npmCommand: ["pnpm"],
+			});
+			packageManager = new DefaultPackageManager({
+				cwd: tempDir,
+				agentDir,
+				settingsManager,
+			});
+
+			const source = "git:github.com/user/repo";
+			const targetDir = join(agentDir, "git", "github.com", "user", "repo");
+			const runCommandSpy = vi
+				.spyOn(packageManager as any, "runCommand")
+				.mockImplementation(async (...callArgs: unknown[]) => {
+					const [command, args] = callArgs as [string, string[]];
+					if (command === "git" && args[0] === "clone") {
+						mkdirSync(targetDir, { recursive: true });
+						writeFileSync(join(targetDir, "package.json"), JSON.stringify({ name: "repo", version: "1.0.0" }));
+					}
+				});
+
+			await packageManager.install(source);
+
+			expect(runCommandSpy).toHaveBeenCalledWith("pnpm", ["install"], { cwd: targetDir });
+		});
+
 		it("should update git package dependencies with --omit=dev", async () => {
 			const source = "git:github.com/user/repo";
 			const targetDir = join(tempDir, ".pi", "git", "github.com", "user", "repo");
@@ -527,6 +554,44 @@ Content`,
 			expect(runCommandSpy).toHaveBeenCalledWith("npm", ["install", "--omit=dev"], { cwd: targetDir });
 		});
 
+		it("should use plain install through npmCommand argv when updating git package dependencies", async () => {
+			settingsManager = SettingsManager.inMemory({
+				npmCommand: ["mise", "exec", "node@20", "--", "pnpm"],
+			});
+			packageManager = new DefaultPackageManager({
+				cwd: tempDir,
+				agentDir,
+				settingsManager,
+			});
+
+			const source = "git:github.com/user/repo";
+			const targetDir = join(tempDir, ".pi", "git", "github.com", "user", "repo");
+			mkdirSync(targetDir, { recursive: true });
+			writeFileSync(join(targetDir, "package.json"), JSON.stringify({ name: "repo", version: "1.0.0" }));
+			settingsManager.setProjectPackages([source]);
+
+			vi.spyOn(packageManager as any, "runCommandCapture").mockImplementation(async (...callArgs: unknown[]) => {
+				const [_command, args] = callArgs as [string, string[]];
+				if (args[0] === "rev-parse" && args[1] === "--abbrev-ref" && args[2] === "@{upstream}") {
+					return "origin/main";
+				}
+				if (args[0] === "rev-parse" && args[1] === "@{upstream}") {
+					return "remote-head";
+				}
+				if (args[0] === "rev-parse" && args[1] === "HEAD") {
+					return "local-head";
+				}
+				throw new Error(`Unexpected runCommandCapture args: ${args.join(" ")}`);
+			});
+			const runCommandSpy = vi.spyOn(packageManager as any, "runCommand").mockResolvedValue(undefined);
+
+			await packageManager.update(source);
+
+			expect(runCommandSpy).toHaveBeenCalledWith("mise", ["exec", "node@20", "--", "pnpm", "install"], {
+				cwd: targetDir,
+			});
+		});
+
 		it("should use npmCommand argv for npm root lookup and invalidate cached root when npmCommand changes", () => {
 			settingsManager = SettingsManager.inMemory({
 				npmCommand: ["mise", "exec", "node@20", "--", "npm"],