diff --git a/CHANGELOG.md b/CHANGELOG.md
index 82abb84b2e..e170cab88e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## Unreleased
+### Fixed
+- Migration of non-bare repositories ([#1213](https://github.com/scm-manager/scm-manager/pull/1213))
+
 ## [2.1.0] - 2020-06-18
 ### Added
 - Option to configure jvm parameter of docker container with env JAVA_OPTS or with arguments ([#1175](https://github.com/scm-manager/scm-manager/pull/1175))
diff --git a/scm-plugins/scm-git-plugin/src/main/java/sonia/scm/repository/update/GitV2UpdateStep.java b/scm-plugins/scm-git-plugin/src/main/java/sonia/scm/repository/update/GitV2UpdateStep.java
index 0bbb479ed6..d805fae53c 100644
--- a/scm-plugins/scm-git-plugin/src/main/java/sonia/scm/repository/update/GitV2UpdateStep.java
+++ b/scm-plugins/scm-git-plugin/src/main/java/sonia/scm/repository/update/GitV2UpdateStep.java
@@ -21,7 +21,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  * SOFTWARE.
  */
-    
+
 package sonia.scm.repository.update;
 
 import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
@@ -38,6 +38,7 @@ import sonia.scm.version.Version;
 import javax.inject.Inject;
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.Files;
 import java.nio.file.Path;
 
 import static sonia.scm.version.Version.parse;
@@ -60,7 +61,8 @@ public class GitV2UpdateStep implements UpdateStep {
       (repositoryId, path) -> {
         Repository repository = repositoryMetadataAccess.read(path);
         if (isGitDirectory(repository)) {
-          try (org.eclipse.jgit.lib.Repository gitRepository = build(path.resolve("data").toFile())) {
+          final Path effectiveGitPath = determineEffectiveGitFolder(path);
+          try (org.eclipse.jgit.lib.Repository gitRepository = build(effectiveGitPath.toFile())) {
             new GitConfigHelper().createScmmConfig(repository, gitRepository);
           } catch (IOException e) {
             throw new UpdateException("could not update repository with id " + repositoryId + " in path " + path, e);
@@ -70,6 +72,18 @@ public class GitV2UpdateStep implements UpdateStep {
     );
   }
 
+  public Path determineEffectiveGitFolder(Path path) {
+    Path bareGitFolder = path.resolve("data");
+    Path nonBareGitFolder = bareGitFolder.resolve(".git");
+    final Path effectiveGitPath;
+    if (Files.exists(nonBareGitFolder)) {
+      effectiveGitPath = nonBareGitFolder;
+    } else {
+      effectiveGitPath = bareGitFolder;
+    }
+    return effectiveGitPath;
+  }
+
   private org.eclipse.jgit.lib.Repository build(File directory) throws IOException {
     return new FileRepositoryBuilder()
       .setGitDir(directory)
diff --git a/scm-plugins/scm-git-plugin/src/test/java/sonia/scm/repository/update/GitV2UpdateStepTest.java b/scm-plugins/scm-git-plugin/src/test/java/sonia/scm/repository/update/GitV2UpdateStepTest.java
new file mode 100644
index 0000000000..c207a4bf54
--- /dev/null
+++ b/scm-plugins/scm-git-plugin/src/test/java/sonia/scm/repository/update/GitV2UpdateStepTest.java
@@ -0,0 +1,92 @@
+/*
+ * MIT License
+ *
+ * Copyright (c) 2020-present Cloudogu GmbH and Contributors
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+
+package sonia.scm.repository.update;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.junit.jupiter.api.io.TempDir;
+import org.mockito.InjectMocks;
+import org.mockito.Mock;
+import org.mockito.junit.jupiter.MockitoExtension;
+import sonia.scm.repository.Repository;
+import sonia.scm.repository.RepositoryLocationResolver;
+import sonia.scm.update.UpdateStepRepositoryMetadataAccess;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.function.BiConsumer;
+
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.doAnswer;
+import static org.mockito.Mockito.when;
+
+@ExtendWith(MockitoExtension.class)
+class GitV2UpdateStepTest {
+
+  @Mock
+  RepositoryLocationResolver locationResolver;
+  @Mock
+  RepositoryLocationResolver.RepositoryLocationResolverInstance<Path> locationResolverInstance;
+  @Mock
+  UpdateStepRepositoryMetadataAccess<Path> repositoryMetadataAccess;
+
+  @InjectMocks
+  GitV2UpdateStep updateStep;
+
+  @BeforeEach
+  void createDataDirectory(@TempDir Path temp) throws IOException {
+    Files.createDirectories(temp.resolve("data"));
+  }
+
+  @BeforeEach
+  void initRepositoryFolder(@TempDir Path temp) {
+    when(locationResolver.forClass(Path.class)).thenReturn(locationResolverInstance);
+    when(repositoryMetadataAccess.read(temp)).thenReturn(new Repository("123", "git", "space", "X"));
+    doAnswer(invocation -> {
+      invocation.getArgument(0, BiConsumer.class).accept("123", temp);
+      return null;
+    }).when(locationResolverInstance).forAllLocations(any());
+  }
+
+  @Test
+  void shouldWriteConfigFileForBareRepositories(@TempDir Path temp) {
+    updateStep.doUpdate();
+
+    assertThat(temp.resolve("data").resolve("config")).exists();
+  }
+
+  @Test
+  void shouldWriteConfigFileForNonBareRepositories(@TempDir Path temp) throws IOException {
+    Files.createDirectories(temp.resolve("data").resolve(".git"));
+
+    updateStep.doUpdate();
+
+    assertThat(temp.resolve("data").resolve("config")).doesNotExist();
+    assertThat(temp.resolve("data").resolve(".git").resolve("config")).exists();
+  }
+}