diff --git a/AtlasToolkit.iss b/AtlasToolkit.iss
index 2d58d92..9be927f 100644
--- a/AtlasToolkit.iss
+++ b/AtlasToolkit.iss
@@ -44,8 +44,9 @@ WizardStyle=modern
 ; installer from running concurrently.
 AppMutex={#MyAppMutex}
 SetupMutex=AtlasToolkitSetupMutex
-; During a silent self-update, close the running app via Restart Manager; the
-; updater cmd handles relaunch, so don't let Inno restart it (avoids double-launch).
+; CloseApplications=yes lets silent self-update shut down the running app via
+; Restart Manager. RestartApplications=no keeps interactive installs on [Run];
+; self-update passes /RESTARTAPPLICATIONS on the command line to relaunch.
 CloseApplications=yes
 RestartApplications=no
 ; Notify the shell when the .atlas association changes (refreshes icons / Open With).
diff --git a/atlas_toolkit/__init__.py b/atlas_toolkit/__init__.py
index 5e1d7b3..02385db 100644
--- a/atlas_toolkit/__init__.py
+++ b/atlas_toolkit/__init__.py
@@ -2,4 +2,4 @@
 
 from __future__ import annotations
 
-__version__ = "0.3.0"
+__version__ = "0.3.1"
diff --git a/atlas_toolkit/app/bridge.py b/atlas_toolkit/app/bridge.py
index e44f2ec..204f6f6 100644
--- a/atlas_toolkit/app/bridge.py
+++ b/atlas_toolkit/app/bridge.py
@@ -482,11 +482,7 @@ def download_update(self) -> dict[str, Any]:
         return self._updates.download()
 
     def restart_and_install_update(self) -> dict[str, Any]:
-        def _close_window() -> None:
-            if self._window:
-                self._window.destroy()
-
-        return self._updates.restart_and_install(on_success=_close_window)
+        return self._updates.restart_and_install()
 
     def _run_update_check(self) -> None:
         try:
diff --git a/atlas_toolkit/update/controller.py b/atlas_toolkit/update/controller.py
index 59f79f8..4163672 100644
--- a/atlas_toolkit/update/controller.py
+++ b/atlas_toolkit/update/controller.py
@@ -10,7 +10,7 @@
 import threading
 import time
 from pathlib import Path
-from typing import Any, Callable, Optional
+from typing import Any, Optional
 
 from atlas_toolkit.app.config import get_config_dir
 from atlas_toolkit.update.updater import (
@@ -23,8 +23,15 @@
 
 log = logging.getLogger(__name__)
 
-_INNO_SILENT_FLAGS = (
-    "/VERYSILENT /SUPPRESSMSGBOXES /NORESTART /CLOSEAPPLICATIONS /NORESTARTAPPLICATIONS"
+# Inno closes the running app (Restart Manager + AppMutex) and relaunches when done.
+# /RESTARTAPPLICATIONS overrides RestartApplications=no in AtlasToolkit.iss so the
+# interactive [Run] entry (skipifsilent) is not used for silent self-update.
+_INNO_SILENT_INSTALL_ARGS = (
+    "/VERYSILENT",
+    "/SUPPRESSMSGBOXES",
+    "/NORESTART",
+    "/CLOSEAPPLICATIONS",
+    "/RESTARTAPPLICATIONS",
 )
 
 
@@ -137,51 +144,16 @@ def is_installed_build() -> bool:
         return False
 
 
-def build_update_script(
+def build_inno_install_command(
     installer_path: Path,
-    target_exe: Path,
-    pid: int,
-    relaunch_args: list[str],
-    release_url: str,
     inno_log_path: Path,
-) -> str:
-    inst = str(installer_path)
-    exe = str(target_exe)
-    log_path = str(inno_log_path)
-    relaunch_suffix = " ".join(f'"{a}"' for a in relaunch_args)
-    success_launch = f'start "" "{exe}" {relaunch_suffix}'.rstrip()
-
-    fail_message = "Update failed: the installer reported an error."
-    fail_args = [
-        "--update-install-failed",
-        "--update-failed-message", f'"{fail_message}"',
-        "--update-failed-log", f'"{log_path}"',
+) -> list[str]:
+    """Argv to run the downloaded Inno Setup installer for silent self-update."""
+    return [
+        str(installer_path),
+        *_INNO_SILENT_INSTALL_ARGS,
+        f"/LOG={inno_log_path}",
     ]
-    if release_url:
-        fail_args += ["--update-release-url", f'"{release_url}"']
-    fail_launch = f'start "" "{exe}" ' + " ".join(fail_args)
-
-    lines = [
-        "@echo off",
-        "setlocal",
-        ":waitloop",
-        f'tasklist /FI "PID eq {pid}" 2>nul | find "{pid}" >nul',
-        "if not errorlevel 1 (",
-        "    ping -n 2 127.0.0.1 >nul",
-        "    goto waitloop",
-        ")",
-        f'"{inst}" {_INNO_SILENT_FLAGS} /LOG="{log_path}"',
-        "if errorlevel 1 goto failed",
-        success_launch,
-        "goto cleanup",
-        ":failed",
-        fail_launch,
-        ":cleanup",
-        f'del /f /q "{inst}" >nul 2>nul',
-        'del /f /q "%~f0" >nul 2>nul',
-        "endlocal",
-    ]
-    return "\r\n".join(lines) + "\r\n"
 
 
 class UpdateController:
@@ -298,11 +270,8 @@ def _progress(downloaded: int, total: Optional[int]) -> None:
                 progress_cb=_progress,
             )
 
-            target_exe = get_running_executable_path()
             metadata = {
                 "installer_path": str(target_installer_path),
-                "target_exe_path": str(target_exe),
-                "relaunch_args": sys.argv[1:],
                 "version": latest.latest_version,
                 "release_url": latest.release_url,
             }
@@ -339,10 +308,7 @@ def _progress(downloaded: int, total: Optional[int]) -> None:
             )
             return {"ok": False, "error": msg}
 
-    def restart_and_install(
-        self,
-        on_success: Callable[[], None],
-    ) -> dict[str, Any]:
+    def restart_and_install(self) -> dict[str, Any]:
         if not is_running_as_exe():
             return {
                 "ok": False,
@@ -362,42 +328,27 @@ def restart_and_install(
                 "error": "Downloaded installer is missing or invalid.",
             }
 
-        target_exe = get_running_executable_path()
-        if not target_exe.exists() or not target_exe.is_file():
-            return {
-                "ok": False,
-                "error": f"Cannot locate executable for relaunch: {target_exe}",
-            }
-
         update_dir = get_update_dir()
         timestamp = time.strftime("%Y%m%d_%H%M%S")
         inno_log_path = update_dir / f"inno_install_{timestamp}.log"
-        script_text = build_update_script(
-            installer_path=installer_path,
-            target_exe=target_exe,
-            pid=os.getpid(),
-            relaunch_args=list(sys.argv[1:]),
-            release_url=self._release_url or "",
-            inno_log_path=inno_log_path,
-        )
-        script_path = update_dir / f"install_update_{timestamp}_{os.getpid()}.cmd"
+        install_cmd = build_inno_install_command(installer_path, inno_log_path)
 
         try:
-            script_path.write_text(script_text, encoding="utf-8")
-            cmd_exe = os.environ.get("COMSPEC") or "cmd"
             popen_kwargs: dict[str, Any] = {
                 "cwd": str(update_dir),
                 "close_fds": True,
             }
             if sys.platform == "win32":
                 popen_kwargs["creationflags"] = (
-                    subprocess.DETACHED_PROCESS | subprocess.CREATE_NEW_PROCESS_GROUP
+                    subprocess.DETACHED_PROCESS
+                    | subprocess.CREATE_NEW_PROCESS_GROUP
+                    | subprocess.CREATE_NO_WINDOW
                 )
             else:
                 popen_kwargs["start_new_session"] = True
 
-            subprocess.Popen([cmd_exe, "/d", "/c", str(script_path)], **popen_kwargs)
-            on_success()
+            subprocess.Popen(install_cmd, **popen_kwargs)
+            log.info("Launched silent installer: %s", installer_path.name)
             return {"ok": True}
         except Exception as e:
             return {
diff --git a/atlas_toolkit/update/updater.py b/atlas_toolkit/update/updater.py
index a2a80fc..dd6288f 100644
--- a/atlas_toolkit/update/updater.py
+++ b/atlas_toolkit/update/updater.py
@@ -44,7 +44,12 @@ class UpdateInfo(NamedTuple):
 
 def is_running_as_exe() -> bool:
     """Check if running as Nuitka-compiled executable."""
-    return "__compiled__" in globals()
+    import sys
+
+    if getattr(sys, "frozen", False):
+        return True
+    main = sys.modules.get("__main__")
+    return main is not None and getattr(main, "__compiled__", None) is not None
 
 
 def get_current_version() -> str:
diff --git a/pyproject.toml b/pyproject.toml
index 806bb0b..f1c63b1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "AtlasToolkit"
-version = "0.3.0"
+version = "0.3.1"
 description = "Spine Atlas Toolkit - Extract, modify, and repack atlas sprites."
 readme = "README.md"
 requires-python = ">=3.11"
diff --git a/uv.lock b/uv.lock
index 89929d8..52bb156 100644
--- a/uv.lock
+++ b/uv.lock
@@ -4,7 +4,7 @@ requires-python = ">=3.11"
 
 [[package]]
 name = "atlastoolkit"
-version = "0.3.0"
+version = "0.3.1"
 source = { editable = "." }
 dependencies = [
     { name = "pillow" },