diff --git a/.gitignore b/.gitignore
index 6db75f232493..d93aa0542744 100644
--- a/.gitignore
+++ b/.gitignore
@@ -308,7 +308,7 @@ platform/windows/godot_res.res
 
 # Visual Studio 2017 and Visual Studio Code workspace folder
 /.vs
-/.vscode
+.vscode/
 
 # Scons progress indicator
 .scons_node_count
diff --git a/modules/mono/editor/GodotSharpTools/Build/BuildSystem.cs b/modules/mono/editor/GodotSharpTools/Build/BuildSystem.cs
index 16beacb45c38..05712c8d75d4 100644
--- a/modules/mono/editor/GodotSharpTools/Build/BuildSystem.cs
+++ b/modules/mono/editor/GodotSharpTools/Build/BuildSystem.cs
@@ -7,6 +7,10 @@
 using System.Runtime.InteropServices;
 using System.Security;
 using Microsoft.Build.Framework;
+using Microsoft.Build.Construction;
+using GodotSharpTools.Project;
+using System.Net;
+using System.Linq;
 
 namespace GodotSharpTools.Build
 {
@@ -90,6 +94,8 @@ public bool Build(string loggerAssemblyPath, string loggerOutputDir, string[] cu
             if (!string.IsNullOrEmpty(frameworkPath))
                 customPropertiesList.Add("FrameworkPathOverride=" + frameworkPath);
 
+            SynchronizeCsproj();
+
             string compilerArgs = BuildArguments(loggerAssemblyPath, loggerOutputDir, customPropertiesList);
 
             ProcessStartInfo startInfo = new ProcessStartInfo(GetMSBuildPath(), compilerArgs);
@@ -150,6 +156,8 @@ public bool BuildAsync(string loggerAssemblyPath, string loggerOutputDir, string
             if (!string.IsNullOrEmpty(frameworkPath))
                 customPropertiesList.Add("FrameworkPathOverride=" + frameworkPath);
 
+            SynchronizeCsproj();
+
             string compilerArgs = BuildArguments(loggerAssemblyPath, loggerOutputDir, customPropertiesList);
 
             ProcessStartInfo startInfo = new ProcessStartInfo(GetMSBuildPath(), compilerArgs);
@@ -189,6 +197,42 @@ public bool BuildAsync(string loggerAssemblyPath, string loggerOutputDir, string
             return true;
         }
 
+        public void SynchronizeCsproj()
+        {
+            string projectDirectory = Path.GetDirectoryName(solution);
+            ProjectRootElement root = ProjectRootElement.Open(solution.Replace(".sln", ".csproj"));
+
+            foreach (var itemGroup in root.ItemGroups)
+            {
+                if (itemGroup.Condition.Length != 0)
+                    continue;
+
+                foreach (var item in itemGroup.Items.ToArray())
+                {
+                    if (item.ItemType == "Compile")
+                    {
+                        // We need to use WebUtility.UrlDecode because paths in .csproj are URL encoded from some reason
+                        if (!File.Exists(Path.Combine(projectDirectory, WebUtility.UrlDecode(item.Include))))
+                        {
+                            itemGroup.RemoveChild(item);
+                        }
+                    }
+                }
+            }
+
+            foreach (string filePath in Directory.EnumerateFiles(projectDirectory, "*.*", SearchOption.AllDirectories))
+            {
+                if (Path.GetExtension(filePath) == ".cs")
+                {
+                    string relativePath = filePath.RelativeToPath(projectDirectory);
+
+                    root.AddItemChecked("Compile", relativePath);
+                }
+            }
+
+            root.Save();
+        }
+
         private string BuildArguments(string loggerAssemblyPath, string loggerOutputDir, List<string> customProperties)
         {
             string arguments = string.Format(@"""{0}"" /v:normal /t:Build ""/p:{1}"" ""/l:{2},{3};{4}""",
diff --git a/modules/mono/editor/GodotSharpTools/Project/ProjectExtensions.cs b/modules/mono/editor/GodotSharpTools/Project/ProjectExtensions.cs
index f00ec5a2adcc..4b939b6bfac5 100644
--- a/modules/mono/editor/GodotSharpTools/Project/ProjectExtensions.cs
+++ b/modules/mono/editor/GodotSharpTools/Project/ProjectExtensions.cs
@@ -32,12 +32,30 @@ public static bool AddItemChecked(this ProjectRootElement root, string itemType,
             if (!root.HasItem(itemType, include))
             {
                 root.AddItem(itemType, include);
+
                 return true;
             }
 
             return false;
         }
 
+        public static void RemoveItem(this ProjectRootElement root, string itemType, string include)
+        {
+            foreach (var itemGroup in root.ItemGroups)
+            {
+                if (itemGroup.Condition.Length != 0)
+                    continue;
+
+                foreach (var item in itemGroup.Items)
+                {
+                    if (item.ItemType == itemType && item.Include == include)
+                    {
+                        itemGroup.RemoveChild(item);
+                    }
+                }
+            }
+        }
+
         public static Guid GetGuid(this ProjectRootElement root)
         {
             foreach (var property in root.Properties)
diff --git a/modules/mono/editor/GodotSharpTools/Project/ProjectUtils.cs b/modules/mono/editor/GodotSharpTools/Project/ProjectUtils.cs
index 6889ea715f5e..eee911d37215 100644
--- a/modules/mono/editor/GodotSharpTools/Project/ProjectUtils.cs
+++ b/modules/mono/editor/GodotSharpTools/Project/ProjectUtils.cs
@@ -10,6 +10,7 @@ public static void AddItemToProjectChecked(string projectPath, string itemType,
         {
             var dir = Directory.GetParent(projectPath).FullName;
             var root = ProjectRootElement.Open(projectPath);
+
             if (root.AddItemChecked(itemType, include.RelativeToPath(dir).Replace("/", "\\")))
                 root.Save();
         }