diff --git a/kotlin-native/.idea/vcs.xml b/kotlin-native/.idea/vcs.xml
new file mode 100644
index 00000000000..abcc2585c24
--- /dev/null
+++ b/kotlin-native/.idea/vcs.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="IssueNavigationConfiguration">
+    <option name="links">
+      <list>
+        <IssueNavigationLink>
+          <option name="issueRegexp" value="((KT|KTI|IDEA)\-(\d+))" />
+          <option name="linkRegexp" value="https://youtrack.jetbrains.com/issue/$1" />
+        </IssueNavigationLink>
+        <IssueNavigationLink>
+          <option name="issueRegexp" value="#(\d+)" />
+          <option name="linkRegexp" value="https://github.com/JetBrains/kotlin-native/issues/$1" />
+        </IssueNavigationLink>
+      </list>
+    </option>
+  </component>
+  <component name="VcsDirectoryMappings">
+    <mapping directory="" vcs="Git" />
+  </component>
+</project>
\ No newline at end of file
diff --git a/kotlin-native/build-tools/src/main/kotlin/org/jetbrains/kotlin/testing/native/GitDownloadTask.kt b/kotlin-native/build-tools/src/main/kotlin/org/jetbrains/kotlin/testing/native/GitDownloadTask.kt
index b576a08e5d4..2fd3507a361 100644
--- a/kotlin-native/build-tools/src/main/kotlin/org/jetbrains/kotlin/testing/native/GitDownloadTask.kt
+++ b/kotlin-native/build-tools/src/main/kotlin/org/jetbrains/kotlin/testing/native/GitDownloadTask.kt
@@ -103,6 +103,9 @@ open class GitDownloadTask @Inject constructor(
 
         // Store info about used revision for the manual up-to-date check.
         upToDateChecker.storeRevisionInfo()
+
+        // Delete the .git directory of the cloned repo to avoid adding it to IDEA's VCS roots.
+        outputDirectory.resolve(".git").deleteRecursively()
     }