diff --git a/modules/mono/editor/Godot.NET.Sdk/Godot.NET.Sdk/Sdk/Sdk.props b/modules/mono/editor/Godot.NET.Sdk/Godot.NET.Sdk/Sdk/Sdk.props
index 4f8faffde24..5febcf3175a 100644
--- a/modules/mono/editor/Godot.NET.Sdk/Godot.NET.Sdk/Sdk/Sdk.props
+++ b/modules/mono/editor/Godot.NET.Sdk/Godot.NET.Sdk/Sdk/Sdk.props
@@ -14,15 +14,15 @@
     <GodotProjectDir Condition=" '$(SolutionDir)' == '' ">$(MSBuildProjectDirectory)</GodotProjectDir>
     <GodotProjectDir>$([MSBuild]::EnsureTrailingSlash('$(GodotProjectDir)'))</GodotProjectDir>
 
-    <!-- Custom output paths for Godot projects. In brief, 'bin\' and 'obj\' are moved to '$(GodotProjectDir)\.mono\temp\'. -->
-    <BaseOutputPath>$(GodotProjectDir).mono\temp\bin\</BaseOutputPath>
-    <OutputPath>$(GodotProjectDir).mono\temp\bin\$(Configuration)\</OutputPath>
+    <!-- Custom output paths for Godot projects. In brief, 'bin\' and 'obj\' are moved to '$(GodotProjectDir)\.godot\mono\temp\'. -->
+    <BaseOutputPath>$(GodotProjectDir).godot\mono\temp\bin\</BaseOutputPath>
+    <OutputPath>$(GodotProjectDir).godot\mono\temp\bin\$(Configuration)\</OutputPath>
     <!--
     Use custom IntermediateOutputPath and BaseIntermediateOutputPath only if it wasn't already set.
     Otherwise the old values may have already been changed by MSBuild which can cause problems with NuGet.
     -->
-    <IntermediateOutputPath Condition=" '$(IntermediateOutputPath)' == '' ">$(GodotProjectDir).mono\temp\obj\$(Configuration)\</IntermediateOutputPath>
-    <BaseIntermediateOutputPath Condition=" '$(BaseIntermediateOutputPath)' == '' ">$(GodotProjectDir).mono\temp\obj\</BaseIntermediateOutputPath>
+    <IntermediateOutputPath Condition=" '$(IntermediateOutputPath)' == '' ">$(GodotProjectDir).godot\mono\temp\obj\$(Configuration)\</IntermediateOutputPath>
+    <BaseIntermediateOutputPath Condition=" '$(BaseIntermediateOutputPath)' == '' ">$(GodotProjectDir).godot\mono\temp\obj\</BaseIntermediateOutputPath>
 
     <!-- Do not append the target framework name to the output path. -->
     <AppendTargetFrameworkToOutputPath>false</AppendTargetFrameworkToOutputPath>
@@ -102,11 +102,11 @@
     -->
     <Reference Include="GodotSharp">
       <Private>false</Private>
-      <HintPath>$(GodotProjectDir).mono\assemblies\$(GodotApiConfiguration)\GodotSharp.dll</HintPath>
+      <HintPath>$(GodotProjectDir).godot\mono\assemblies\$(GodotApiConfiguration)\GodotSharp.dll</HintPath>
     </Reference>
     <Reference Include="GodotSharpEditor" Condition=" '$(Configuration)' == 'Debug' ">
       <Private>false</Private>
-      <HintPath>$(GodotProjectDir).mono\assemblies\$(GodotApiConfiguration)\GodotSharpEditor.dll</HintPath>
+      <HintPath>$(GodotProjectDir).godot\mono\assemblies\$(GodotApiConfiguration)\GodotSharpEditor.dll</HintPath>
     </Reference>
   </ItemGroup>
 </Project>
diff --git a/modules/mono/editor/GodotTools/GodotTools.IdeMessaging/Client.cs b/modules/mono/editor/GodotTools/GodotTools.IdeMessaging/Client.cs
index 572c5414129..0f50c905317 100644
--- a/modules/mono/editor/GodotTools/GodotTools.IdeMessaging/Client.cs
+++ b/modules/mono/editor/GodotTools/GodotTools.IdeMessaging/Client.cs
@@ -121,7 +121,7 @@ namespace GodotTools.IdeMessaging
             this.messageHandler = messageHandler;
             this.logger = logger;
 
-            string projectMetadataDir = Path.Combine(godotProjectDir, ".mono", "metadata");
+            string projectMetadataDir = Path.Combine(godotProjectDir, ".godot", "mono", "metadata");
 
             MetaFilePath = Path.Combine(projectMetadataDir, GodotIdeMetadata.DefaultFileName);
 
diff --git a/modules/mono/godotsharp_dirs.cpp b/modules/mono/godotsharp_dirs.cpp
index 692da991c7d..df31823deb7 100644
--- a/modules/mono/godotsharp_dirs.cpp
+++ b/modules/mono/godotsharp_dirs.cpp
@@ -122,7 +122,7 @@ public:
 
 private:
 	_GodotSharpDirs() {
-		res_data_dir = "res://.mono";
+		res_data_dir = "res://.godot/mono";
 		res_metadata_dir = res_data_dir.plus_file("metadata");
 		res_assemblies_base_dir = res_data_dir.plus_file("assemblies");
 		res_assemblies_dir = res_assemblies_base_dir.plus_file(GDMono::get_expected_api_build_config());