diff --git a/misc/scripts/install_accesskit.py b/misc/scripts/install_accesskit.py
index 2d2789b728..41bb7a7706 100755
--- a/misc/scripts/install_accesskit.py
+++ b/misc/scripts/install_accesskit.py
@@ -14,7 +14,7 @@ sys.path.insert(0, os.path.join(os.path.dirname(os.path.abspath(__file__)), "../
 # Base Godot dependencies path
 # If cross-compiling (no LOCALAPPDATA), we install in `bin`
 deps_folder = os.getenv("LOCALAPPDATA")
-if deps_folder:
+if deps_folder and not os.getenv("MSYSTEM"):
     deps_folder = os.path.join(deps_folder, "Godot", "build_deps")
 else:
     deps_folder = os.path.join("bin", "build_deps")
diff --git a/misc/scripts/install_angle.py b/misc/scripts/install_angle.py
index abfafcec68..0d5fff8183 100755
--- a/misc/scripts/install_angle.py
+++ b/misc/scripts/install_angle.py
@@ -13,7 +13,7 @@ from misc.utility.color import Ansi, color_print
 # Base Godot dependencies path
 # If cross-compiling (no LOCALAPPDATA), we install in `bin`
 deps_folder = os.getenv("LOCALAPPDATA")
-if deps_folder:
+if deps_folder and not os.getenv("MSYSTEM"):
     deps_folder = os.path.join(deps_folder, "Godot", "build_deps")
 else:
     deps_folder = os.path.join("bin", "build_deps")
diff --git a/misc/scripts/install_d3d12_sdk_windows.py b/misc/scripts/install_d3d12_sdk_windows.py
index 135b8d8fe5..43474ec327 100755
--- a/misc/scripts/install_d3d12_sdk_windows.py
+++ b/misc/scripts/install_d3d12_sdk_windows.py
@@ -25,7 +25,7 @@ args = parser.parse_args()
 # Base Godot dependencies path
 # If cross-compiling (no LOCALAPPDATA), we install in `bin`
 deps_folder = os.getenv("LOCALAPPDATA")
-if deps_folder:
+if deps_folder and not os.getenv("MSYSTEM"):
     deps_folder = os.path.join(deps_folder, "Godot", "build_deps")
 else:
     deps_folder = os.path.join("bin", "build_deps")
diff --git a/misc/scripts/install_winrt.py b/misc/scripts/install_winrt.py
index fa03a5dac3..ba1c87ffbf 100755
--- a/misc/scripts/install_winrt.py
+++ b/misc/scripts/install_winrt.py
@@ -14,7 +14,7 @@ sys.path.insert(0, os.path.join(os.path.dirname(os.path.abspath(__file__)), "../
 # Base Godot dependencies path
 # If cross-compiling (no LOCALAPPDATA), we install in `bin`
 deps_folder = os.getenv("LOCALAPPDATA")
-if deps_folder:
+if deps_folder and not os.getenv("MSYSTEM"):
     deps_folder = os.path.join(deps_folder, "Godot", "build_deps")
 else:
     deps_folder = os.path.join("bin", "build_deps")
diff --git a/platform/windows/detect.py b/platform/windows/detect.py
index 50807536fa..4f6a726bf8 100644
--- a/platform/windows/detect.py
+++ b/platform/windows/detect.py
@@ -205,7 +205,7 @@ def get_opts():
 
     # Dependencies folder.
     deps_folder = os.getenv("LOCALAPPDATA")
-    if deps_folder:
+    if deps_folder and not os.getenv("MSYSTEM"):
         deps_folder = os.path.join(deps_folder, "Godot", "build_deps")
     else:
         # Cross-compiling, the deps install script puts things in `bin`.