diff --git a/modules/integration/src/test/scala/scala/cli/integration/CompileScalacCompatTestDefinitions.scala b/modules/integration/src/test/scala/scala/cli/integration/CompileScalacCompatTestDefinitions.scala
index 872924ae58..a862818e58 100644
--- a/modules/integration/src/test/scala/scala/cli/integration/CompileScalacCompatTestDefinitions.scala
+++ b/modules/integration/src/test/scala/scala/cli/integration/CompileScalacCompatTestDefinitions.scala
@@ -205,4 +205,36 @@ trait CompileScalacCompatTestDefinitions { _: CompileTestDefinitions =>
         }
       }
   }
+
+  {
+    val prefixes = Seq("-", "--")
+    for {
+      prefix1 <- prefixes
+      prefix2 <- prefixes
+      optionKey = "Werror"
+      option1   = prefix1 + optionKey
+      option2   = prefix2 + optionKey
+      if actualScalaVersion.startsWith("3")
+    } test(
+      s"allow to override $option1 compiler option passed via directive by passing $option2 from the command line"
+    ) {
+      val file = "example.scala"
+      TestInputs(os.rel / file ->
+        s"""//> using options -Wunused:all $option1
+           |@main def main() = {
+           |  val unused = ""
+           |  println("Hello, world!")
+           |}
+           |""".stripMargin).fromRoot { root =>
+        os.proc(
+          TestUtil.cli,
+          "compile",
+          file,
+          s"$option2:false",
+          extraOptions
+        )
+          .call(cwd = root, stderr = os.Pipe)
+      }
+    }
+  }
 }
diff --git a/modules/options/src/main/scala/scala/build/options/ShadowingSeq.scala b/modules/options/src/main/scala/scala/build/options/ShadowingSeq.scala
index 1ff88b5daf..820c9fa844 100644
--- a/modules/options/src/main/scala/scala/build/options/ShadowingSeq.scala
+++ b/modules/options/src/main/scala/scala/build/options/ShadowingSeq.scala
@@ -31,7 +31,12 @@ final case class ShadowingSeq[T] private (values: Seq[Seq[T]]) {
       for (group <- values.iterator ++ other.iterator) {
         assert(group.nonEmpty)
         val keyOpt = key.makeKey(group)
-        if (!keyOpt.exists(seen.contains)) {
+        if !keyOpt.exists {
+            case k if k.startsWith("--") => seen.contains(k) || seen.contains(k.stripPrefix("-"))
+            case k if k.startsWith("-")  => seen.contains(k) || seen.contains(s"-$k")
+            case k                       => seen.contains(k)
+          }
+        then {
           l += group
           for (key <- keyOpt)
             seen += key