diff --git a/core/runtime/src/main/java/io/quarkus/runtime/configuration/ConfigDiagnostic.java b/core/runtime/src/main/java/io/quarkus/runtime/configuration/ConfigDiagnostic.java
index 574ae74cf169e..d073ca201d7f9 100644
--- a/core/runtime/src/main/java/io/quarkus/runtime/configuration/ConfigDiagnostic.java
+++ b/core/runtime/src/main/java/io/quarkus/runtime/configuration/ConfigDiagnostic.java
@@ -6,6 +6,7 @@
 import java.net.URI;
 import java.nio.file.DirectoryStream;
 import java.nio.file.Files;
+import java.nio.file.NotDirectoryException;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.Collections;
@@ -186,6 +187,9 @@ public static Set<String> configFiles(Path configFilesLocation) throws IOExcepti
             for (Path candidate : candidates) {
                 configFiles.add(candidate.toUri().toURL().toString());
             }
+        } catch (NotDirectoryException ignored) {
+            log.debugf("File %s is not a directory", configFilesLocation.toAbsolutePath());
+            return Collections.emptySet();
         }
         return configFiles;
     }