diff --git a/modules/cli/src/main/scala/scala/cli/commands/shared/ScalacOptions.scala b/modules/cli/src/main/scala/scala/cli/commands/shared/ScalacOptions.scala
index 62e772f500..ce73e08edc 100644
--- a/modules/cli/src/main/scala/scala/cli/commands/shared/ScalacOptions.scala
+++ b/modules/cli/src/main/scala/scala/cli/commands/shared/ScalacOptions.scala
@@ -101,16 +101,16 @@ object ScalacOptions {
           case h :: t
               if scalacOptionsPrefixes.exists(h.startsWith) &&
               !ScalacDeprecatedOptions.contains(h) =>
-            Right(Some((Some(h :: acc.getOrElse(Nil)), t)))
+            Right(Some((Some(acc.getOrElse(Nil) :+ h), t)))
           case h :: t if scalacNoArgAliasedOptions.contains(h) =>
-            Right(Some((Some(h :: acc.getOrElse(Nil)), t)))
+            Right(Some((Some(acc.getOrElse(Nil) :+ h), t)))
           case h :: t if scalacAliasedOptions.contains(h) =>
             // check if the next scalac arg is a different option or a param to the current option
             val maybeOptionArg = t.headOption.filter(!_.startsWith("-"))
             // if it's a param, it'll be treated as such and considered already parsed
             val newTail = maybeOptionArg.map(_ => t.drop(1)).getOrElse(t)
             val newHead = List(h) ++ maybeOptionArg
-            Right(Some((Some(newHead ++ acc.getOrElse(Nil)), newTail)))
+            Right(Some((Some(acc.getOrElse(Nil) ++ newHead), newTail)))
           case _ => underlying.step(args, index, acc, formatter)
         }
       def get(acc: Option[List[String]], formatter: Formatter[Name]): Either[Error, List[String]] =
diff --git a/modules/integration/src/test/scala/scala/cli/integration/SipScalaTests.scala b/modules/integration/src/test/scala/scala/cli/integration/SipScalaTests.scala
index 86e8a6ca2d..e0e637f610 100644
--- a/modules/integration/src/test/scala/scala/cli/integration/SipScalaTests.scala
+++ b/modules/integration/src/test/scala/scala/cli/integration/SipScalaTests.scala
@@ -515,6 +515,52 @@ class SipScalaTests extends ScalaCliSuite with SbtTestHelper with MillTestHelper
     }
   }
 
+  for {
+    useDirective <- Seq(true, false)
+    if !Properties.isWin
+    optionsSource = if (useDirective) "using directive" else "command line"
+  } test(s"consecutive -Wconf:* flags are not ignored (passed via $optionsSource)") {
+    val sv                 = "3.5.2"
+    val sourceFileName     = "example.scala"
+    val warningConfOptions = Seq("-Wconf:cat=deprecation:e", "-Wconf:any:s")
+    val maybeDirectiveString =
+      if (useDirective) s"//> using options ${warningConfOptions.mkString(" ")}" else ""
+    TestInputs(os.rel / sourceFileName ->
+      s"""//> using scala $sv
+         |$maybeDirectiveString
+         |object WConfExample extends App {
+         |  @deprecated("This method will be removed", "1.0.0")
+         |  def oldMethod(): Unit = println("This is an old method.")
+         |  oldMethod()
+         |}
+         |""".stripMargin).fromRoot { root =>
+      val localCache = root / "local-cache"
+      val localBin   = root / "local-bin"
+      os.proc(
+        TestUtil.cs,
+        "install",
+        "--cache",
+        localCache,
+        "--install-dir",
+        localBin,
+        s"scalac:$sv"
+      ).call(cwd = root)
+      val cliRes =
+        os.proc(
+          TestUtil.cli,
+          "compile",
+          sourceFileName,
+          "--server=false",
+          if (useDirective) Nil else warningConfOptions
+        )
+          .call(cwd = root, check = false, stderr = os.Pipe)
+      val scalacRes = os.proc(localBin / "scalac", warningConfOptions, sourceFileName)
+        .call(cwd = root, check = false, stderr = os.Pipe)
+      expect(scalacRes.exitCode == cliRes.exitCode)
+      expect(cliRes.err.trim() == scalacRes.err.trim())
+    }
+  }
+
   for {
     sv <- Seq(Constants.scala212, Constants.scala213, Constants.scala3NextRc)
     code =
diff --git a/modules/options/src/main/scala/scala/build/options/ScalacOpt.scala b/modules/options/src/main/scala/scala/build/options/ScalacOpt.scala
index 6fbcb86a84..a03d53f474 100644
--- a/modules/options/src/main/scala/scala/build/options/ScalacOpt.scala
+++ b/modules/options/src/main/scala/scala/build/options/ScalacOpt.scala
@@ -18,7 +18,8 @@ object ScalacOpt {
   private val repeatingKeys = Set(
     "-Xplugin",
     "-P", // plugin options
-    "-language"
+    "-language",
+    "-Wconf"
   )
 
   implicit val hashedType: HashedType[ScalacOpt] = {