diff --git a/Wabbajack.Lib/AInstaller.cs b/Wabbajack.Lib/AInstaller.cs
index ce4550d4..27efbcb0 100644
--- a/Wabbajack.Lib/AInstaller.cs
+++ b/Wabbajack.Lib/AInstaller.cs
@@ -377,6 +377,30 @@ namespace Wabbajack.Lib
               .Where(d => d != null)
               .Do(d => indexed.Remove(d.To));
 
+            Utils.Log("Cleaning empty folders");
+            var expectedFolders = indexed.Keys.SelectMany(path =>
+            {
+                // Get all the folders and all the folder parents
+                // so for foo\bar\baz\qux.txt this emits ["foo", "foo\\bar", "foo\\bar\\baz"]
+                var split = path.Split('\\');
+                return Enumerable.Range(1, split.Length - 1).Select(t => string.Join("\\", split.Take(t)));
+            }).Distinct()
+              .Select(p => Path.Combine(OutputFolder, p))
+              .ToHashSet();
+
+            try
+            {
+                Directory.EnumerateDirectories(OutputFolder, DirectoryEnumerationOptions.Recursive)
+                    .Where(p => !expectedFolders.Contains(p))
+                    .OrderByDescending(p => p.Length)
+                    .Do(p => Directory.Delete(p));
+            }
+            catch (Exception)
+            {
+                // ignored because it's not worth throwing a fit over
+                Utils.Log("Error when trying to clean empty folders. This doesn't really matter.");
+            }
+
             UpdateTracker.NextStep("Updating Modlist");
             Utils.Log($"Optimized {ModList.Directives.Count} directives to {indexed.Count} required");
             var requiredArchives = indexed.Values.OfType<FromArchive>()
diff --git a/Wabbajack.Test/SanityTests.cs b/Wabbajack.Test/SanityTests.cs
index 411ad9d3..e2f9c732 100644
--- a/Wabbajack.Test/SanityTests.cs
+++ b/Wabbajack.Test/SanityTests.cs
@@ -1,5 +1,6 @@
 using System;
 using System.Collections.Generic;
+using System.IO;
 using System.Linq;
 using System.Threading.Tasks;
 using Microsoft.VisualStudio.TestTools.UnitTesting;
@@ -87,6 +88,11 @@ namespace Wabbajack.Test
             var extra_path = utils.PathOfInstalledFile(mod, @"something_i_made.foo");
             File.WriteAllText(extra_path, "bleh");
 
+            var extra_folder = Path.Combine(Path.GetDirectoryName(utils.PathOfInstalledFile(mod, @"something_i_made.foo")), "folder_i_made");
+            Directory.CreateDirectory(extra_folder);
+            
+            Assert.IsTrue(Directory.Exists(extra_folder));
+
 
             var unchanged_modified = File.GetLastWriteTime(unchanged_path);
             var modified_modified = File.GetLastWriteTime(modified_path);
@@ -105,6 +111,7 @@ namespace Wabbajack.Test
             Assert.AreEqual(unchanged_modified, File.GetLastWriteTime(unchanged_path));
             Assert.AreNotEqual(modified_modified, File.GetLastWriteTime(modified_path));
             Assert.IsFalse(File.Exists(extra_path));
+            Assert.IsFalse(Directory.Exists(extra_folder));
         }