diff --git a/src/GitHub.Api/Git/TreeData.cs b/src/GitHub.Api/Git/TreeData.cs
index ac9e67b2c..997cbffed 100644
--- a/src/GitHub.Api/Git/TreeData.cs
+++ b/src/GitHub.Api/Git/TreeData.cs
@@ -7,6 +7,7 @@ public interface ITreeData
     {
         string Path { get; }
         bool IsActive { get; }
+        bool IsChecked { get; }
     }
 
     [Serializable]
@@ -64,6 +65,7 @@ public bool Equals(GitBranchTreeData other)
 
         public string Path => GitBranch.Name;
         public bool IsActive => isActive;
+        public bool IsChecked => false;
     }
 
     [Serializable]
@@ -73,11 +75,13 @@ public struct GitStatusEntryTreeData : ITreeData
 
         public GitStatusEntry gitStatusEntry;
         public bool isLocked;
+        public bool isChecked;
 
         public GitStatusEntryTreeData(GitStatusEntry gitStatusEntry, bool isLocked = false)
         {
             this.isLocked = isLocked;
             this.gitStatusEntry = gitStatusEntry;
+            isChecked = gitStatusEntry.Staged;
         }
 
         public override int GetHashCode()
@@ -127,5 +131,6 @@ public bool Equals(GitStatusEntryTreeData other)
         public GitStatusEntry GitStatusEntry => gitStatusEntry;
         public GitFileStatus FileStatus => gitStatusEntry.Status;
         public bool IsLocked => isLocked;
+        public bool IsChecked => isChecked;
     }
-}
\ No newline at end of file
+}
diff --git a/src/GitHub.Api/UI/TreeBase.cs b/src/GitHub.Api/UI/TreeBase.cs
index 4804558ce..57c299ed5 100644
--- a/src/GitHub.Api/UI/TreeBase.cs
+++ b/src/GitHub.Api/UI/TreeBase.cs
@@ -118,7 +118,7 @@ public void Load(IEnumerable<TData> treeDatas)
                         {
                             isActive = treeData.IsActive;
                             treeNodeTreeData = treeData;
-                            isChecked = isCheckable && checkedFiles.Contains(nodePath);
+                            isChecked = isCheckable && (checkedFiles.Contains(nodePath) || treeData.IsChecked);
                         }
 
                         isSelected = selectedNodePath != null && nodePath == selectedNodePath;
diff --git a/src/UnityExtension/Assets/Editor/GitHub.Unity/UI/ChangesView.cs b/src/UnityExtension/Assets/Editor/GitHub.Unity/UI/ChangesView.cs
index d905fb070..0d6235b42 100644
--- a/src/UnityExtension/Assets/Editor/GitHub.Unity/UI/ChangesView.cs
+++ b/src/UnityExtension/Assets/Editor/GitHub.Unity/UI/ChangesView.cs
@@ -478,7 +478,7 @@ private void Commit()
         {
             isBusy = true;
             var files = treeChanges.GetCheckedFiles().ToList();
-            ITask addTask;
+            ITask addTask = null;
 
             if (files.Count == gitStatusEntries.Count)
             {
@@ -486,11 +486,18 @@ private void Commit()
             }
             else
             {
-                addTask = Repository.CommitFiles(files, commitMessage, commitBody);
+                ITask commit = Repository.CommitFiles(files, commitMessage, commitBody);
+
+                // if there are files that have been staged outside of Unity, but they aren't selected for commit, remove them
+                // from the index before commiting, otherwise the commit will take them along.
+                var filesStagedButNotChecked = gitStatusEntries.Where(x => x.Staged).Select(x => x.Path).Except(files).ToList();
+                if (filesStagedButNotChecked.Count > 0)
+                    addTask = GitClient.Remove(filesStagedButNotChecked);
+                addTask = addTask == null ? commit : addTask.Then(commit);
             }
 
             addTask
-                .FinallyInUI((success, exception) => 
+                .FinallyInUI((success, exception) =>
                     {
                         if (success)
                         {
diff --git a/src/tests/UnitTests/UI/TreeBaseTests.cs b/src/tests/UnitTests/UI/TreeBaseTests.cs
index e2e5e07ed..60110e39c 100644
--- a/src/tests/UnitTests/UI/TreeBaseTests.cs
+++ b/src/tests/UnitTests/UI/TreeBaseTests.cs
@@ -35,6 +35,7 @@ public struct TestTreeData : ITreeData
 
         public string Path { get; set; }
         public bool IsActive { get; set; }
+        public bool IsChecked { get; set; }
 
         public override string ToString()
         {