diff --git a/base/src/META-INF/blaze-base.xml b/base/src/META-INF/blaze-base.xml
index b37d79ac279..69bce8f2321 100644
--- a/base/src/META-INF/blaze-base.xml
+++ b/base/src/META-INF/blaze-base.xml
@@ -342,6 +342,9 @@
     <registryKey defaultValue="true"
                  description="Enables opening the project view file the first time the project is imported"
                  key="bazel.project.import.open_project_view"/>
+    <registryKey defaultValue="false"
+                 description="Scan for non-root source folders in source jars. (requires re-sync)"
+                 key="bazel.sync.detect.source.roots"/>
   </extensions>
 
   <extensions defaultExtensionNs="com.intellij">
diff --git a/base/src/com/google/idea/blaze/base/model/LibraryFilesProvider.java b/base/src/com/google/idea/blaze/base/model/LibraryFilesProvider.java
index c71ba17a8ed..32e60156675 100644
--- a/base/src/com/google/idea/blaze/base/model/LibraryFilesProvider.java
+++ b/base/src/com/google/idea/blaze/base/model/LibraryFilesProvider.java
@@ -16,9 +16,12 @@
 package com.google.idea.blaze.base.model;
 
 import com.google.common.collect.ImmutableList;
+import com.google.idea.blaze.base.sync.libraries.LibraryModifier;
 import com.intellij.openapi.roots.libraries.Library;
 import java.io.File;
 
+import static com.google.common.collect.ImmutableList.toImmutableList;
+
 /** Provides files to be updated in {@link Library.ModifiableModel}. */
 public interface LibraryFilesProvider {
   /** Returns the name of library that the modifier will update. */
@@ -30,12 +33,32 @@ public interface LibraryFilesProvider {
    */
   ImmutableList<File> getClassFiles(BlazeProjectData blazeProjectData);
 
+  /**
+   * Returns a list of files' urls that should be added to {@link Library.ModifiableModel} as
+   * OrderRootType.CLASSES.
+   */
+  default ImmutableList<String> getClassFilesUrls(BlazeProjectData blazeProjectData) {
+    return getClassFiles(blazeProjectData).stream()
+            .map(LibraryModifier::pathToUrl)
+            .collect(toImmutableList());
+  };
+
   /**
    * Returns a list of files that should be added to {@link Library.ModifiableModel} as
    * OrderRootType.SOURCES.
    */
   ImmutableList<File> getSourceFiles(BlazeProjectData blazeProjectData);
 
+  /**
+   * Returns a list of files' urls that should be added to {@link Library.ModifiableModel} as
+   * OrderRootType.SOURCES.
+   */
+  default ImmutableList<String> getSourceFilesUrls(BlazeProjectData blazeProjectData) {
+    return getSourceFiles(blazeProjectData).stream()
+            .map(LibraryModifier::pathToUrl)
+            .collect(toImmutableList());
+  }
+
   default boolean supportAnchors() {
     return false;
   }
diff --git a/base/src/com/google/idea/blaze/base/sync/libraries/LibraryModifier.java b/base/src/com/google/idea/blaze/base/sync/libraries/LibraryModifier.java
index 1597cb7dd40..539d79b6a45 100644
--- a/base/src/com/google/idea/blaze/base/sync/libraries/LibraryModifier.java
+++ b/base/src/com/google/idea/blaze/base/sync/libraries/LibraryModifier.java
@@ -26,6 +26,7 @@
 import com.intellij.openapi.util.io.FileUtil;
 import com.intellij.openapi.util.io.FileUtilRt;
 import com.intellij.openapi.vfs.StandardFileSystems;
+import com.intellij.openapi.vfs.VirtualFile;
 import com.intellij.openapi.vfs.VirtualFileManager;
 import com.intellij.util.io.URLUtil;
 import java.io.File;
@@ -49,12 +50,12 @@ public Library.ModifiableModel getModifiableModel() {
   /** Writes the library content to its {@link Library.ModifiableModel}. */
   public void updateModifiableModel(BlazeProjectData blazeProjectData) {
     removeAllContents();
-    for (File classFile : libraryFilesProvider.getClassFiles(blazeProjectData)) {
-      addRoot(classFile, OrderRootType.CLASSES);
+    for (String classFileUrl : libraryFilesProvider.getClassFilesUrls(blazeProjectData)) {
+      addRoot(classFileUrl, OrderRootType.CLASSES);
     }
 
-    for (File sourceFile : libraryFilesProvider.getSourceFiles(blazeProjectData)) {
-      addRoot(sourceFile, OrderRootType.SOURCES);
+    for (String sourceFileUrl : libraryFilesProvider.getSourceFilesUrls(blazeProjectData)) {
+      addRoot(sourceFileUrl, OrderRootType.SOURCES);
     }
   }
 
@@ -68,15 +69,16 @@ private ModifiableModel getLibraryModifiableModel(
     return modelsProvider.getModifiableLibraryModel(library);
   }
 
-  private void addRoot(File file, OrderRootType orderRootType) {
-    if (!file.exists()) {
-      logger.warn("No local file found for " + file);
+  private void addRoot(String fileUrl, OrderRootType orderRootType) {
+    VirtualFile virtualFile = VirtualFileManager.getInstance().findFileByUrl(fileUrl);
+    if (virtualFile == null || !virtualFile.exists()) {
+      logger.warn("No local file found for " + fileUrl);
       return;
     }
-    modifiableModel.addRoot(pathToUrl(file), orderRootType);
+    modifiableModel.addRoot(fileUrl, orderRootType);
   }
 
-  private String pathToUrl(File path) {
+  public static String pathToUrl(File path) {
     String name = path.getName();
     boolean isJarFile =
         FileUtilRt.extensionEquals(name, "jar")
diff --git a/java/src/com/google/idea/blaze/java/sync/model/BlazeJarLibrary.java b/java/src/com/google/idea/blaze/java/sync/model/BlazeJarLibrary.java
index eeda2c03bf8..76f3918f72d 100644
--- a/java/src/com/google/idea/blaze/java/sync/model/BlazeJarLibrary.java
+++ b/java/src/com/google/idea/blaze/java/sync/model/BlazeJarLibrary.java
@@ -19,6 +19,7 @@
 
 import com.google.common.collect.ImmutableList;
 import com.google.devtools.intellij.model.ProjectData;
+import com.google.idea.blaze.base.async.executor.ProgressiveTaskWithProgressIndicator;
 import com.google.idea.blaze.base.ideinfo.LibraryArtifact;
 import com.google.idea.blaze.base.ideinfo.ProtoWrapper;
 import com.google.idea.blaze.base.ideinfo.TargetKey;
@@ -26,12 +27,22 @@
 import com.google.idea.blaze.base.model.BlazeProjectData;
 import com.google.idea.blaze.base.model.LibraryFilesProvider;
 import com.google.idea.blaze.base.model.LibraryKey;
+import com.google.idea.blaze.base.sync.libraries.LibraryModifier;
 import com.google.idea.blaze.java.libraries.AttachedSourceJarManager;
 import com.google.idea.blaze.java.libraries.JarCache;
 import com.intellij.openapi.diagnostic.Logger;
 import com.intellij.openapi.project.Project;
+import com.intellij.openapi.roots.ui.configuration.JavaVfsSourceRootDetectionUtil;
+import com.intellij.openapi.util.registry.Registry;
+import com.intellij.openapi.vfs.VirtualFile;
+import com.intellij.openapi.vfs.VirtualFileManager;
+
 import java.io.File;
+import java.util.Collections;
+import java.util.LinkedList;
+import java.util.List;
 import java.util.Objects;
+import java.util.concurrent.ExecutionException;
 import javax.annotation.Nullable;
 import javax.annotation.concurrent.Immutable;
 
@@ -140,6 +151,36 @@ public ImmutableList<File> getSourceFiles(BlazeProjectData blazeProjectData) {
           .collect(toImmutableList());
     }
 
+    @Override
+    public ImmutableList<String> getSourceFilesUrls(BlazeProjectData blazeProjectData) {
+      final ImmutableList<File> sourceFiles = getSourceFiles(blazeProjectData);
+      ImmutableList<String> jarFilesAsSourceRoots = sourceFiles.stream().map(LibraryModifier::pathToUrl).collect(toImmutableList());
+      if (!Registry.is("bazel.sync.detect.source.roots")) {
+        return jarFilesAsSourceRoots;
+      } else {
+        try {
+          return ProgressiveTaskWithProgressIndicator.builder(project, "Locating source roots in source path entry")
+                  .setModality(ProgressiveTaskWithProgressIndicator.Modality.MODAL)
+                  .submitTaskWithResult(indicator -> {
+                    List<String> sourceFilesUrls = new LinkedList<>();
+                    for (File sourceFile : sourceFiles) {
+                      VirtualFile jarFile = VirtualFileManager.getInstance().findFileByUrl(LibraryModifier.pathToUrl(sourceFile));
+                      List<VirtualFile> candidates = Collections.emptyList();
+                      if (jarFile != null && jarFile.exists()) {
+                        candidates = JavaVfsSourceRootDetectionUtil.suggestRoots(jarFile, indicator);
+                      }
+                      if (!candidates.isEmpty()) {
+                        candidates.forEach(sourceVirtualFile -> sourceFilesUrls.add(sourceVirtualFile.getUrl()));
+                      }
+                    }
+                    return ImmutableList.copyOf(sourceFilesUrls);
+                  }).get();
+        } catch (InterruptedException | ExecutionException e) {
+          return jarFilesAsSourceRoots;
+        }
+      }
+    }
+
     @Override
     public boolean equals(Object other) {
       if (this == other) {