diff --git a/lib/overcommit/hook_context/pre_commit.rb b/lib/overcommit/hook_context/pre_commit.rb
index 094bba2a..289eaffe 100644
--- a/lib/overcommit/hook_context/pre_commit.rb
+++ b/lib/overcommit/hook_context/pre_commit.rb
@@ -18,9 +18,9 @@ def setup_environment
       if !initial_commit? && any_changes?
         @stash_attempted = true
 
+        stash_message = "Overcommit: Stash of repo state before hook run at #{Time.now}"
         result = Overcommit::Utils.execute(
-          %w[git stash save --keep-index --quiet] +
-          ["Overcommit: Stash of repo state before hook run at #{Time.now}"]
+          %w[git stash save --keep-index --quiet] + [stash_message]
         )
 
         unless result.success?
@@ -31,8 +31,7 @@ def setup_environment
                 "\nSTDOUT:#{result.stdout}\nSTDERR:#{result.stderr}"
         end
 
-        # False if only submodule references were changed
-        @changes_stashed = modified_files.any?
+        @changes_stashed = `git stash list -1`.include?(stash_message)
       end
 
       # While running the hooks make it appear as if nothing changed
diff --git a/spec/overcommit/hook_context/pre_commit_spec.rb b/spec/overcommit/hook_context/pre_commit_spec.rb
index cdf3f8ba..b1af2d0e 100644
--- a/spec/overcommit/hook_context/pre_commit_spec.rb
+++ b/spec/overcommit/hook_context/pre_commit_spec.rb
@@ -53,7 +53,7 @@
 
       it 'keeps staged changes' do
         subject
-        File.open('tracked-file', 'r').read.should == "Hello World\nSome more text\n"
+        `git show :tracked-file`.should == "Hello World\nSome more text\n"
       end
 
       it 'keeps untracked files' do
@@ -119,13 +119,21 @@
       around do |example|
         repo do
           `echo "Hello World" > tracked-file`
-          `git add tracked-file`
-          `git commit -m "Add tracked-file"`
+          `echo "Hello Other World" > other-tracked-file`
+          `git add tracked-file other-tracked-file`
+          `git commit -m "Add tracked-file and other-tracked-file"`
           `echo "Hello Again" > untracked-file`
+          `echo "Some more text" >> other-tracked-file`
           example.run
         end
       end
 
+      it 'restores the unstaged changes' do
+        subject
+        File.open('other-tracked-file', 'r').read.
+          should == "Hello Other World\nSome more text\n"
+      end
+
       it 'keeps already-committed files' do
         subject
         File.open('tracked-file', 'r').read.should == "Hello World\n"
@@ -162,6 +170,11 @@
           should == "Hello World\nSome more text\nYet some more text\n"
       end
 
+      it 'keeps staged changes' do
+        subject
+        `git show :tracked-file`.should == "Hello World\nSome more text\n"
+      end
+
       it 'keeps untracked files' do
         subject
         File.open('untracked-file', 'r').read.should == "Hello Again\n"
@@ -213,6 +226,36 @@
         }.from(false)
       end
     end
+
+    context 'when submodule changes were staged along with other changes' do
+      around do |example|
+        submodule = repo do
+          `git commit --allow-empty -m "Initial commit"`
+        end
+
+        repo do
+          `git submodule add #{submodule} sub &>/dev/null`
+          `git commit -m "Add submodule"`
+          `echo "Hello World" > sub/submodule-file`
+          `git submodule foreach 'git add submodule-file'`
+          `git submodule foreach 'git commit -m "Another commit"'`
+          `echo "Hello Again" > tracked-file`
+          `git add sub tracked-file`
+          example.run
+        end
+      end
+
+      it 'keeps staged submodule change' do
+        expect { subject }.to_not change {
+          (`git diff --cached` =~ /-Subproject commit[\s\S]*\+Subproject commit/).nil?
+        }.from(false)
+      end
+
+      it 'keeps staged file change' do
+        subject
+        `git show :tracked-file`.should == "Hello Again\n"
+      end
+    end
   end
 
   describe '#modified_files' do