diff --git a/extension/jdtls.ext/com.microsoft.gradle.bs.importer/src/com/microsoft/gradle/bs/importer/GradleBuildServerProjectImporter.java b/extension/jdtls.ext/com.microsoft.gradle.bs.importer/src/com/microsoft/gradle/bs/importer/GradleBuildServerProjectImporter.java
index 9cf4c3997..218dc2db0 100644
--- a/extension/jdtls.ext/com.microsoft.gradle.bs.importer/src/com/microsoft/gradle/bs/importer/GradleBuildServerProjectImporter.java
+++ b/extension/jdtls.ext/com.microsoft.gradle.bs.importer/src/com/microsoft/gradle/bs/importer/GradleBuildServerProjectImporter.java
@@ -9,6 +9,7 @@
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.concurrent.CompletionException;
+import java.util.stream.Collectors;
 
 import org.eclipse.core.internal.resources.Project;
 import org.eclipse.core.internal.resources.ProjectDescription;
@@ -150,13 +151,6 @@ public boolean applies(Collection<IPath> projectConfigurations, IProgressMonitor
 
     @Override
     public void importToWorkspace(IProgressMonitor monitor) throws OperationCanceledException, CoreException {
-        IPath rootPath = ResourceUtils.filePathFromURI(rootFolder.toURI().toString());
-        BuildServerConnection buildServer = ImporterPlugin.getBuildServerConnection(rootPath, true);
-        if (buildServer == null) {
-            JavaLanguageServerPlugin.logError("Reach the maximum number of attempts to connect to the build server, use BuildShip instead");
-            this.isResolved = false;
-            return;
-        }
         // for all the path in this.directories, find the out most directory which belongs
         // to rootFolder and use that directory as the root folder for the build server.
         // TODO: consider the following folder structure
@@ -166,11 +160,42 @@ public void importToWorkspace(IProgressMonitor monitor) throws OperationCanceled
         //    |-- sub3
         // if user partially selects sub1 and sub2, we should still use ROOT as the root folder
         // and only import sub1 and sub2 as projects.
-        java.nio.file.Path inferredRoot = this.directories.stream()
+        java.nio.file.Path inferredRoot = null;
+        List<java.nio.file.Path> sortedDirectories = this.directories.stream()
                 .filter(directory -> directory.startsWith(rootFolder.toPath()))
                 .sorted((p1, p2) -> p1.getNameCount() - p2.getNameCount())
-                .findFirst()
-                .orElse(rootFolder.toPath());
+                .collect(Collectors.toList());
+        if (sortedDirectories.isEmpty()) {
+            inferredRoot = null; // theoretically this should not happen
+        } else if (sortedDirectories.size() == 1) {
+            inferredRoot = sortedDirectories.get(0);
+        } else {
+            if (sortedDirectories.get(0).getNameCount() == sortedDirectories.get(1).getNameCount()) {
+                // if there are multiple directories with the same name count, we can't determine
+                // the root folder for the build server.
+                Telemetry telemetry = new Telemetry("unableToDetermineRootFolder", "true");
+                Utils.sendTelemetry(JavaLanguageServerPlugin.getProjectsManager().getConnection(),
+                        telemetry);
+                inferredRoot = null;
+            } else {
+                inferredRoot = sortedDirectories.get(0);
+            }
+        }
+
+        if (inferredRoot == null) {
+            JavaLanguageServerPlugin.logError("Failed to determine the root folder for the build server, use BuildShip instead");
+            this.isResolved = false;
+            return;
+        }
+
+        IPath rootPath = ResourceUtils.filePathFromURI(rootFolder.toURI().toString());
+        BuildServerConnection buildServer = ImporterPlugin.getBuildServerConnection(rootPath, true);
+        if (buildServer == null) {
+            JavaLanguageServerPlugin.logError("Reach the maximum number of attempts to connect to the build server, use BuildShip instead");
+            this.isResolved = false;
+            return;
+        }
+
         InitializeBuildParams params = new InitializeBuildParams(
                 CLIENT_NAME,
                 ImporterPlugin.getBundleVersion(),