diff --git a/src/extension/extension.cpp b/src/extension/extension.cpp
index 3b0b24a..76b4e0b 100644
--- a/src/extension/extension.cpp
+++ b/src/extension/extension.cpp
@@ -93,11 +93,11 @@ static struct runtime_config_t {
 
 		// `python_home_path`
 		if(likely_running_from_editor) {
-			python_home_path = lib_dir_path;
+			python_home_path = lib_dir_path / "python";
 		}
 		else {
 			auto platform_arch = std::string(PYGODOT_PLATFORM) + "-" + std::string(PYGODOT_ARCH);
-			python_home_path = lib_dir_path / "lib" / platform_arch;
+			python_home_path = lib_dir_path / "lib" / platform_arch / "python";
 		}
 	}
 } runtime_config;
@@ -171,12 +171,13 @@ static bool init_python_isolated() {
 	auto py_version = py_major + "." + py_minor;
 	auto py_version_no_dot = py_major + py_minor;
 	auto python_zip_name = "python" + py_version_no_dot + ".zip";
+    auto python_lib_path = runtime_config.python_home_path / "lib";
 	auto python_lib_name = "python" + py_version;
 
 	add_module_search_path((runtime_config.python_home_path / python_zip_name).string());
-	add_module_search_path((runtime_config.python_home_path / python_lib_name).string());
-	add_module_search_path((runtime_config.python_home_path / python_lib_name / "lib-dynload").string());
-	add_module_search_path((runtime_config.python_home_path / python_lib_name / "site-packages").string());
+	add_module_search_path((python_lib_path / python_lib_name).string());
+	add_module_search_path((python_lib_path / python_lib_name / "lib-dynload").string());
+	add_module_search_path((python_lib_path / python_lib_name / "site-packages").string());
 
 	config.module_search_paths_set = 1;
 
diff --git a/tools/build/prepare_python.py b/tools/build/prepare_python.py
index 651f36f..618fa7c 100644
--- a/tools/build/prepare_python.py
+++ b/tools/build/prepare_python.py
@@ -17,6 +17,7 @@ class PlatformConfig:
 	ext_suffixes: list[str]
 	so_path: str
 	python_lib_dir: str
+	python_bin_paths: list[str]
 	python_ext_dir: str
 	executable: str
 
@@ -42,6 +43,7 @@ def add_platform_config(*args, **kwargs):
 	ext_suffixes = ['.so'],
 	so_path = 'lib/libpython3.12.so.1.0',
 	python_lib_dir = 'lib/python3.12',
+	python_bin_paths = ['bin'],
 	python_ext_dir = 'lib/python3.12/lib-dynload',
 	executable = 'bin/python3.12',
 )
@@ -55,6 +57,7 @@ def add_platform_config(*args, **kwargs):
 	ext_suffixes = ['.dll', '.pyd'],
 	so_path = 'python312.dll',
 	python_lib_dir = 'Lib',
+	python_bin_paths = ['python.exe', 'pythonw.exe'],
 	python_ext_dir = 'DLLs',
 	executable = 'python.exe',
 )
@@ -68,6 +71,7 @@ def add_platform_config(*args, **kwargs):
 	ext_suffixes = ['.so'],
 	so_path = 'lib/libpython3.12.dylib',
 	python_lib_dir = 'lib/python3.12',
+	python_bin_paths = ['bin'],
 	python_ext_dir = 'lib/python3.12/lib-dynload',
 	executable = 'bin/python3.12',
 )
@@ -81,6 +85,7 @@ def add_platform_config(*args, **kwargs):
 	ext_suffixes = ['.so'],
 	so_path = 'lib/libpython3.12.dylib',
 	python_lib_dir = 'lib/python3.12',
+	python_bin_paths = ['bin'],
 	python_ext_dir = 'lib/python3.12/lib-dynload',
 	executable = 'bin/python3.12',
 )
@@ -105,32 +110,41 @@ def prepare_for_platform(platform: str, arch: str,
 
 	shutil.unpack_archive(src_dir / pathlib.Path(config.source_url).name, extract_dir = src_dir)
 
-	src = src_dir / 'python'
-	src_lib_path = src / config.so_path
+	src_python = src_dir / 'python'
+	src_lib_path = src_python / config.so_path
 	lib_filename = pathlib.Path(config.so_path).name
 
 	if platform == 'macos':
 		# Rename the library id (which we depend on) to be in @rpath.
 		# (it defaults to /install/lib/)
-		subprocess.run(['install_name_tool', '-id', f'@rpath/{lib_filename}', src_lib_path], check=True)
+		subprocess.run(['install_name_tool', '-id', f'@rpath/python/lib/{lib_filename}', src_lib_path], check=True)
+
 
-	dest_dir.mkdir(parents=True, exist_ok=True)
-	shutil.copy2(src_lib_path, dest_dir)
+	dest_dir_python = dest_dir / 'python'
+	dest_dir_python_lib = dest_dir_python / 'lib'
+	dest_dir_python_lib.mkdir(parents=True, exist_ok=True)
 
+	shutil.copy2(src_lib_path, dest_dir_python_lib)
 	if platform == 'macos':
-		subprocess.run(['strip', '-x', dest_dir / lib_filename], check=True)
+		subprocess.run(['strip', '-x', dest_dir_python_lib / lib_filename], check=True)
 	else:
-		subprocess.run(['strip', '-s', dest_dir / lib_filename], check=True)
+		subprocess.run(['strip', '-s', dest_dir_python_lib / lib_filename], check=True)
+
+	for bin_path in config.python_bin_paths:
+		shutil.copytree(src_python / bin_path, dest_dir_python / bin_path, dirs_exist_ok=True)
+		if bin_path == 'bin':
+			# Ignore the bin path in Godot.
+			open(dest_dir_python / bin_path / '.gdignore', 'a').close()
 
-	if (src / config.python_ext_dir).exists():
-		dest_ext_dir = dest_dir / 'python3.12' / 'lib-dynload'
+	if (src_python / config.python_ext_dir).exists():
+		dest_ext_dir = dest_dir_python_lib / 'python3.12' / 'lib-dynload'
 		dest_ext_dir.mkdir(parents=True, exist_ok=True)
 
-		for path in (src / config.python_ext_dir).iterdir():
+		for path in (src_python / config.python_ext_dir).iterdir():
 			if any(suffix in path.suffixes for suffix in config.ext_suffixes):
 				shutil.copy2(path, dest_ext_dir)
 
-	shutil.make_archive(dest_dir / 'python312', 'zip', root_dir=src / config.python_lib_dir, base_dir='')
+	shutil.make_archive(dest_dir / 'python312', 'zip', root_dir=src_python / config.python_lib_dir, base_dir='')
 
 
 def get_python_for_platform(platform: str, arch: str, src_dir: pathlib.Path) -> pathlib.Path: