diff --git a/scm-plugins/scm-git-plugin/src/main/java/sonia/scm/repository/spi/AbstractGitCommand.java b/scm-plugins/scm-git-plugin/src/main/java/sonia/scm/repository/spi/AbstractGitCommand.java
index 396ec525a3..2531888a8b 100644
--- a/scm-plugins/scm-git-plugin/src/main/java/sonia/scm/repository/spi/AbstractGitCommand.java
+++ b/scm-plugins/scm-git-plugin/src/main/java/sonia/scm/repository/spi/AbstractGitCommand.java
@@ -38,6 +38,7 @@ import com.google.common.base.Strings;
 import org.apache.shiro.SecurityUtils;
 import org.apache.shiro.subject.Subject;
 import org.eclipse.jgit.api.Git;
+import org.eclipse.jgit.api.Status;
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.RefNotFoundException;
 import org.eclipse.jgit.lib.ObjectId;
@@ -214,10 +215,11 @@ class AbstractGitCommand
       }
     }
 
-    Optional<RevCommit> doCommit(String message, Person author, boolean isMergeCommit) {
+    Optional<RevCommit> doCommit(String message, Person author) {
       Person authorToUse = determineAuthor(author);
       try {
-        if (isMergeCommit || !clone.status().call().isClean()) {
+        Status status = clone.status().call();
+        if (!status.isClean() || isInMerge()) {
           return of(clone.commit()
             .setAuthor(authorToUse.getName(), authorToUse.getMail())
             .setMessage(message)
@@ -225,11 +227,15 @@ class AbstractGitCommand
         } else {
           return empty();
         }
-      } catch (GitAPIException e) {
+      } catch (GitAPIException | IOException e) {
         throw new InternalRepositoryException(context.getRepository(), "could not commit changes", e);
       }
     }
 
+    private boolean isInMerge() throws IOException {
+      return clone.getRepository().readMergeHeads() != null && !clone.getRepository().readMergeHeads().isEmpty();
+    }
+
     void push() {
       try {
         clone.push().call();
diff --git a/scm-plugins/scm-git-plugin/src/main/java/sonia/scm/repository/spi/GitMergeCommand.java b/scm-plugins/scm-git-plugin/src/main/java/sonia/scm/repository/spi/GitMergeCommand.java
index 6e30239fed..5643c858b5 100644
--- a/scm-plugins/scm-git-plugin/src/main/java/sonia/scm/repository/spi/GitMergeCommand.java
+++ b/scm-plugins/scm-git-plugin/src/main/java/sonia/scm/repository/spi/GitMergeCommand.java
@@ -99,7 +99,7 @@ public class GitMergeCommand extends AbstractGitCommand implements MergeCommand
 
     private void doCommit() {
       logger.debug("merged branch {} into {}", toMerge, target);
-      doCommit(MessageFormat.format(determineMessageTemplate(), toMerge, target), author, true);
+      doCommit(MessageFormat.format(determineMessageTemplate(), toMerge, target), author);
     }
 
     private String determineMessageTemplate() {
diff --git a/scm-plugins/scm-git-plugin/src/main/java/sonia/scm/repository/spi/GitModifyCommand.java b/scm-plugins/scm-git-plugin/src/main/java/sonia/scm/repository/spi/GitModifyCommand.java
index 2c48329e98..a68be0a4da 100644
--- a/scm-plugins/scm-git-plugin/src/main/java/sonia/scm/repository/spi/GitModifyCommand.java
+++ b/scm-plugins/scm-git-plugin/src/main/java/sonia/scm/repository/spi/GitModifyCommand.java
@@ -62,7 +62,7 @@ public class GitModifyCommand extends AbstractGitCommand implements ModifyComman
         r.execute(this);
       }
       failIfNotChanged(() -> new NoChangesMadeException(repository, ModifyWorker.this.request.getBranch()));
-      Optional<RevCommit> revCommit = doCommit(request.getCommitMessage(), request.getAuthor(), false);
+      Optional<RevCommit> revCommit = doCommit(request.getCommitMessage(), request.getAuthor());
       push();
       return revCommit.orElseThrow(() -> new NoChangesMadeException(repository, ModifyWorker.this.request.getBranch())).name();
     }
diff --git a/scm-plugins/scm-git-plugin/src/test/java/sonia/scm/repository/spi/GitMergeCommandTest.java b/scm-plugins/scm-git-plugin/src/test/java/sonia/scm/repository/spi/GitMergeCommandTest.java
index cb1ee140d5..5586a2f710 100644
--- a/scm-plugins/scm-git-plugin/src/test/java/sonia/scm/repository/spi/GitMergeCommandTest.java
+++ b/scm-plugins/scm-git-plugin/src/test/java/sonia/scm/repository/spi/GitMergeCommandTest.java
@@ -84,6 +84,26 @@ public class GitMergeCommandTest extends AbstractGitCommandTestBase {
 
   @Test
   public void shouldAllowEmptyMergeCommit() throws IOException, GitAPIException {
+    GitMergeCommand command = createCommand();
+    MergeCommandRequest request = new MergeCommandRequest();
+    request.setTargetBranch("master");
+    request.setBranchToMerge("empty_merge");
+    request.setAuthor(new Person("Dirk Gently", "dirk@holistic.det"));
+
+    MergeCommandResult mergeCommandResult = command.merge(request);
+
+    assertThat(mergeCommandResult.isSuccess()).isTrue();
+
+    Repository repository = createContext().open();
+    Iterable<RevCommit> commits = new Git(repository).log().add(repository.resolve("master")).setMaxCount(1).call();
+    RevCommit mergeCommit = commits.iterator().next();
+    assertThat(mergeCommit.getParentCount()).isEqualTo(2);
+    assertThat(mergeCommit.getParent(0).name()).isEqualTo("fcd0ef1831e4002ac43ea539f4094334c79ea9ec");
+    assertThat(mergeCommit.getParent(1).name()).isEqualTo("d81ad6c63d7e2162308d69637b339dedd1d9201c");
+  }
+
+  @Test
+  public void shouldNotMergeTwice() throws IOException, GitAPIException {
     GitMergeCommand command = createCommand();
     MergeCommandRequest request = new MergeCommandRequest();
     request.setTargetBranch("master");
@@ -103,7 +123,7 @@ public class GitMergeCommandTest extends AbstractGitCommandTestBase {
 
     ObjectId secondMergeCommit = new Git(repository).log().add(repository.resolve("master")).setMaxCount(1).call().iterator().next().getId();
 
-    assertThat(firstMergeCommit).isNotEqualTo(secondMergeCommit);
+    assertThat(secondMergeCommit).isEqualTo(firstMergeCommit);
   }
 
   @Test
diff --git a/scm-plugins/scm-git-plugin/src/test/resources/sonia/scm/repository/spi/scm-git-spi-test.zip b/scm-plugins/scm-git-plugin/src/test/resources/sonia/scm/repository/spi/scm-git-spi-test.zip
index addda86090..4310e63733 100644
Binary files a/scm-plugins/scm-git-plugin/src/test/resources/sonia/scm/repository/spi/scm-git-spi-test.zip and b/scm-plugins/scm-git-plugin/src/test/resources/sonia/scm/repository/spi/scm-git-spi-test.zip differ