diff --git a/MediaBrowser.Server.Implementations/FileOrganization/TvFolderOrganizer.cs b/MediaBrowser.Server.Implementations/FileOrganization/TvFolderOrganizer.cs
index 83fca9939..81f767e91 100644
--- a/MediaBrowser.Server.Implementations/FileOrganization/TvFolderOrganizer.cs
+++ b/MediaBrowser.Server.Implementations/FileOrganization/TvFolderOrganizer.cs
@@ -46,6 +46,8 @@ namespace MediaBrowser.Server.Implementations.FileOrganization
                 .Where(i => _libraryManager.IsVideoFile(i.FullName) && i.Length >= minFileBytes)
                 .ToList();
 
+            var processedFolders = new HashSet<string>();
+
             progress.Report(10);
 
             if (eligibleFiles.Count > 0)
@@ -59,7 +61,11 @@ namespace MediaBrowser.Server.Implementations.FileOrganization
 
                     try
                     {
-                        await organizer.OrganizeEpisodeFile(file.FullName, options, options.OverwriteExistingEpisodes, cancellationToken).ConfigureAwait(false);
+                        var result = await organizer.OrganizeEpisodeFile(file.FullName, options, options.OverwriteExistingEpisodes, cancellationToken).ConfigureAwait(false);
+                        if (result.Status == FileSortingStatus.Success && !processedFolders.Contains(file.DirectoryName))
+                        {
+                            processedFolders.Add(file.DirectoryName);
+                        }
                     }
                     catch (Exception ex)
                     {
@@ -77,7 +83,7 @@ namespace MediaBrowser.Server.Implementations.FileOrganization
             cancellationToken.ThrowIfCancellationRequested();
             progress.Report(99);
 
-            foreach (var path in watchLocations)
+            foreach (var path in processedFolders)
             {
                 var deleteExtensions = options.LeftOverFileExtensionsToDelete
                     .Select(i => i.Trim().TrimStart('.'))
@@ -92,9 +98,9 @@ namespace MediaBrowser.Server.Implementations.FileOrganization
 
                 if (options.DeleteEmptyFolders)
                 {
-                    foreach (var subfolder in GetDirectories(path).ToList())
+                    if (!IsWatchFolder(path, watchLocations))
                     {
-                        DeleteEmptyFolders(subfolder);
+                        DeleteEmptyFolders(path);
                     }
                 }
             }
@@ -102,27 +108,6 @@ namespace MediaBrowser.Server.Implementations.FileOrganization
             progress.Report(100);
         }
 
-        /// <summary>
-        /// Gets the directories.
-        /// </summary>
-        /// <param name="path">The path.</param>
-        /// <returns>IEnumerable{System.String}.</returns>
-        private IEnumerable<string> GetDirectories(string path)
-        {
-            try
-            {
-                return _fileSystem
-                    .GetDirectoryPaths(path)
-                    .ToList();
-            }
-            catch (IOException ex)
-            {
-                _logger.ErrorException("Error getting files from {0}", ex, path);
-
-                return new List<string>();
-            }
-        }
-
         /// <summary>
         /// Gets the files to organize.
         /// </summary>
@@ -195,5 +180,26 @@ namespace MediaBrowser.Server.Implementations.FileOrganization
             }
             catch (UnauthorizedAccessException) { }
         }
+
+        /// <summary>
+        /// Determines if a given folder path is contained in a folder list
+        /// </summary>
+        /// <param name="path">The folder path to check.</param>
+        /// <param name="watchLocations">A list of folders.</param>
+        private bool IsWatchFolder(string path, IEnumerable<string> watchLocations)
+        {
+            // Use GetFullPath to resolve 8.3 naming and path indirections
+            path = Path.GetFullPath(path);
+
+            foreach (var watchFolder in watchLocations)
+            {
+                if (String.Equals(path, Path.GetFullPath(watchFolder), StringComparison.OrdinalIgnoreCase))
+                {
+                    return true;
+                }
+            }
+
+            return false;
+        }
     }
 }