diff --git a/joern-cli/frontends/javasrc2cpg/src/test/scala/io/joern/javasrc2cpg/passes/ConfigFileCreationPassTests.scala b/joern-cli/frontends/javasrc2cpg/src/test/scala/io/joern/javasrc2cpg/passes/ConfigFileCreationPassTests.scala
index 46412c53a87e..941245ef5663 100644
--- a/joern-cli/frontends/javasrc2cpg/src/test/scala/io/joern/javasrc2cpg/passes/ConfigFileCreationPassTests.scala
+++ b/joern-cli/frontends/javasrc2cpg/src/test/scala/io/joern/javasrc2cpg/passes/ConfigFileCreationPassTests.scala
@@ -61,4 +61,25 @@ class ConfigFileCreationPassTests extends JavaSrcCode2CpgFixture {
     }
   }
 
+  "it should populate config files correctly when they are nested" in {
+    val configFile1Path = Paths.get("config.properties").toString
+    val configFile2Path = Paths.get("someDir", "config.properties").toString
+    val cpg = code("""public class Foo{}
+        |""".stripMargin)
+      .moreCode(code = "config.file=1", fileName = configFile1Path)
+      .moreCode(code = "config.file=2", fileName = configFile2Path)
+
+    cpg.typeDecl.name("Foo").nonEmpty shouldBe true
+    cpg.configFile.sortBy(_.name).l match {
+      case List(configFile1, configFile2) =>
+        configFile1.name shouldBe configFile1Path
+        configFile1.content shouldBe "config.file=1"
+
+        configFile2.name shouldBe configFile2Path
+        configFile2.content shouldBe "config.file=2"
+
+      case result => fail(s"Expected two config files but got $result")
+    }
+  }
+
 }
diff --git a/joern-cli/frontends/x2cpg/src/main/scala/io/joern/x2cpg/passes/frontend/XConfigFileCreationPass.scala b/joern-cli/frontends/x2cpg/src/main/scala/io/joern/x2cpg/passes/frontend/XConfigFileCreationPass.scala
index 27ca76ae5115..a8a6d984cda9 100644
--- a/joern-cli/frontends/x2cpg/src/main/scala/io/joern/x2cpg/passes/frontend/XConfigFileCreationPass.scala
+++ b/joern-cli/frontends/x2cpg/src/main/scala/io/joern/x2cpg/passes/frontend/XConfigFileCreationPass.scala
@@ -55,7 +55,7 @@ abstract class XConfigFileCreationPass(cpg: Cpg, private val rootDir: Option[Str
   }
 
   private def configFileName(configFile: File): String = {
-    Try(Paths.get(rootDir.get).toAbsolutePath)
+    Try(Paths.get(rootDir.getOrElse(cpg.metaData.root.head)).toAbsolutePath)
       .map(_.relativize(configFile.path.toAbsolutePath).toString)
       .getOrElse(configFile.name)
   }