diff --git a/scalalib/src/mill/scalalib/ScalaModule.scala b/scalalib/src/mill/scalalib/ScalaModule.scala
index c499dda5e0e..adc22bf4f73 100644
--- a/scalalib/src/mill/scalalib/ScalaModule.scala
+++ b/scalalib/src/mill/scalalib/ScalaModule.scala
@@ -130,7 +130,7 @@ trait ScalaModule extends JavaModule { outer =>
     } yield p.toNIO.toString
 
     val pluginOptions = scalacPluginClasspath().map(pluginPathRef => s"-Xplugin:${pluginPathRef.path}")
-    val options = Seq("-d", javadocDir.toNIO.toString, "-usejavacp") ++ pluginOptions
+    val options = Seq("-d", javadocDir.toNIO.toString, "-usejavacp") ++ pluginOptions ++ scalacOptions()
 
     if (files.nonEmpty) subprocess(
       "scala.tools.nsc.ScalaDoc",
@@ -193,5 +193,3 @@ trait ScalaModule extends JavaModule { outer =>
   override def artifactId: T[String] = artifactName() + artifactSuffix()
 
 }
-
-
diff --git a/scalalib/test/resources/hello-world-flags/core/src/Main.scala b/scalalib/test/resources/hello-world-flags/core/src/Main.scala
new file mode 100644
index 00000000000..c23ee8eda9a
--- /dev/null
+++ b/scalalib/test/resources/hello-world-flags/core/src/Main.scala
@@ -0,0 +1,6 @@
+import scala.collection.immutable.SortedMap
+
+object Main extends App {
+  def foo[F[_], A](fa: F[A]): String = fa.toString
+  foo { x: Int => x * 2 }
+}
\ No newline at end of file
diff --git a/scalalib/test/src/mill/scalalib/HelloWorldTests.scala b/scalalib/test/src/mill/scalalib/HelloWorldTests.scala
index f1342d04ba9..46cf82de84b 100644
--- a/scalalib/test/src/mill/scalalib/HelloWorldTests.scala
+++ b/scalalib/test/src/mill/scalalib/HelloWorldTests.scala
@@ -130,6 +130,16 @@ object HelloWorldTests extends TestSuite {
     }
   }
 
+  object HelloWorldFlags extends HelloBase{
+    object core extends ScalaModule {
+      def scalaVersion = "2.12.4"
+      
+      def scalacOptions = super.scalacOptions() ++ Seq(
+        "-Ypartial-unification"
+      )
+    }
+  }
+
   object HelloScalacheck extends HelloBase{
     object foo extends ScalaModule {
       def scalaVersion = "2.12.4"
@@ -523,6 +533,25 @@ object HelloWorldTests extends TestSuite {
       }
     }
 
+    'flags - {
+      // make sure flags are passed when compiling/running
+      'runMain - workspaceTest(
+        HelloWorldFlags,
+        resourcePath = pwd / 'scalalib / 'test / 'resources / "hello-world-flags"
+      ){ eval =>
+        val Right((_, evalCount)) = eval.apply(HelloWorldFlags.core.runMain("Main"))
+        assert(evalCount > 0)
+      }
+      // make sure flags are passed during ScalaDoc generation
+      'docJar - workspaceTest(
+        HelloWorldFlags,
+        resourcePath = pwd / 'scalalib / 'test / 'resources / "hello-world-flags"
+      ){ eval =>
+        val Right((_, evalCount)) = eval.apply(HelloWorldFlags.core.docJar)
+        assert(evalCount > 0)
+      }
+    }
+
     'scalacheck - workspaceTest(
       HelloScalacheck,
       resourcePath = pwd / 'scalalib / 'test / 'resources / "hello-scalacheck"