diff --git a/lib/overcommit/git_repo.rb b/lib/overcommit/git_repo.rb
index 1af73e81..1f30759f 100644
--- a/lib/overcommit/git_repo.rb
+++ b/lib/overcommit/git_repo.rb
@@ -158,9 +158,12 @@ def store_merge_state
       # conflict. This is necessary since stashing removes the merge state.
       if merge_head != 'MERGE_HEAD'
         @merge_head = merge_head
+
+        merge_mode_file = Overcommit::Utils.git_path('MERGE_MODE')
+        @merge_mode = File.open(merge_mode_file).read if File.exist?(merge_mode_file)
       end
 
-      merge_msg_file = File.expand_path('MERGE_MSG', Overcommit::Utils.git_dir)
+      merge_msg_file = Overcommit::Utils.git_path('MERGE_MSG')
       @merge_msg = File.open(merge_msg_file).read if File.exist?(merge_msg_file)
     end
 
@@ -182,17 +185,20 @@ def store_cherry_pick_state
     # of a merge.
     def restore_merge_state
       if @merge_head
-        FileUtils.touch(File.expand_path('MERGE_MODE', Overcommit::Utils.git_dir))
+        File.open(Overcommit::Utils.git_path('MERGE_MODE'), 'w') do |f|
+          f.write(@merge_mode || '')
+        end
+        @merge_mode = nil
 
-        File.open(File.expand_path('MERGE_HEAD', Overcommit::Utils.git_dir), 'w') do |f|
+        File.open(Overcommit::Utils.git_path('MERGE_HEAD'), 'w') do |f|
           f.write(@merge_head)
         end
         @merge_head = nil
       end
 
       if @merge_msg
-        File.open(File.expand_path('MERGE_MSG', Overcommit::Utils.git_dir), 'w') do |f|
-          f.write("#{@merge_msg}\n")
+        File.open(Overcommit::Utils.git_path('MERGE_MSG'), 'w') do |f|
+          f.write(@merge_msg)
         end
         @merge_msg = nil
       end
@@ -202,8 +208,7 @@ def restore_merge_state
     # of a cherry-pick.
     def restore_cherry_pick_state
       if @cherry_head
-        File.open(File.expand_path('CHERRY_PICK_HEAD',
-                                   Overcommit::Utils.git_dir), 'w') do |f|
+        File.open(Overcommit::Utils.git_path('CHERRY_PICK_HEAD'), 'w') do |f|
           f.write(@cherry_head)
         end
         @cherry_head = nil
diff --git a/lib/overcommit/utils.rb b/lib/overcommit/utils.rb
index b315edac..ab5f1246 100644
--- a/lib/overcommit/utils.rb
+++ b/lib/overcommit/utils.rb
@@ -74,6 +74,31 @@ def git_dir
           end
       end
 
+      # Returns an absolute path to a file in the current worktree's Git
+      # directory.
+      #
+      # @param path [String]
+      # @return [String]
+      def git_path(path)
+        cmd = %w[git rev-parse]
+        if GIT_VERSION < '2.5'
+          cmd << '--git-dir'
+        else
+          cmd += ['--git-path', path]
+        end
+
+        result = execute(cmd)
+        unless result.success?
+          raise Overcommit::Exceptions::InvalidGitRepo,
+                'Unable to determine Git path. ' \
+                'Not a recognizable Git repository!'
+        end
+
+        resolved_path = result.stdout.chomp("\n")
+        resolved_path = File.join(resolved_path, path) if GIT_VERSION < '2.5'
+        File.expand_path(resolved_path, Dir.pwd)
+      end
+
       # Remove ANSI escape sequences from a string.
       #
       # This is useful for stripping colorized output from external tools.
diff --git a/spec/overcommit/git_repo_spec.rb b/spec/overcommit/git_repo_spec.rb
index b887415b..29fc52fd 100644
--- a/spec/overcommit/git_repo_spec.rb
+++ b/spec/overcommit/git_repo_spec.rb
@@ -320,6 +320,58 @@
     end
   end
 
+  describe 'operation state in a linked worktree',
+           if: Overcommit::GIT_VERSION >= '2.5' do
+    around do |example|
+      repo do
+        `git commit --allow-empty -m "Initial commit"`
+        linked_worktree = File.join(File.dirname(Dir.pwd), 'linked-worktree')
+        result = Overcommit::Utils.execute(
+          %W[git worktree add -b linked-worktree #{linked_worktree}],
+        )
+        raise "Unable to create worktree: #{result.stderr}" unless result.success?
+
+        Dir.chdir(linked_worktree) { example.run }
+      end
+    end
+
+    let(:git_dir) { File.expand_path(`git rev-parse --git-dir`.chomp) }
+    let(:common_dir) { File.expand_path(`git rev-parse --git-common-dir`.chomp) }
+    let(:head) { `git rev-parse HEAD`.chomp }
+
+    it 'restores merge state only to the linked worktree' do
+      merge_message = "Merge linked branch\n"
+      File.write(File.join(git_dir, 'MERGE_HEAD'), head)
+      File.write(File.join(git_dir, 'MERGE_MODE'), 'no-ff')
+      File.write(File.join(git_dir, 'MERGE_MSG'), merge_message)
+
+      described_class.store_merge_state
+      FileUtils.rm(
+        %w[MERGE_HEAD MERGE_MODE MERGE_MSG].
+          map { |file| File.join(git_dir, file) },
+      )
+      described_class.restore_merge_state
+
+      File.read(File.join(git_dir, 'MERGE_HEAD')).should == head
+      File.read(File.join(git_dir, 'MERGE_MODE')).should == 'no-ff'
+      File.read(File.join(git_dir, 'MERGE_MSG')).should == merge_message
+      File.exist?(File.join(common_dir, 'MERGE_HEAD')).should == false
+      File.exist?(File.join(common_dir, 'MERGE_MODE')).should == false
+      File.exist?(File.join(common_dir, 'MERGE_MSG')).should == false
+    end
+
+    it 'restores cherry-pick state only to the linked worktree' do
+      File.write(File.join(git_dir, 'CHERRY_PICK_HEAD'), head)
+
+      described_class.store_cherry_pick_state
+      FileUtils.rm(File.join(git_dir, 'CHERRY_PICK_HEAD'))
+      described_class.restore_cherry_pick_state
+
+      File.read(File.join(git_dir, 'CHERRY_PICK_HEAD')).should == head
+      File.exist?(File.join(common_dir, 'CHERRY_PICK_HEAD')).should == false
+    end
+  end
+
   describe '.staged_submodule_removals' do
     subject { described_class.staged_submodule_removals }