diff --git a/modules/build/src/main/scala/scala/build/CrossSources.scala b/modules/build/src/main/scala/scala/build/CrossSources.scala
index 362ad844ba..c96449d667 100644
--- a/modules/build/src/main/scala/scala/build/CrossSources.scala
+++ b/modules/build/src/main/scala/scala/build/CrossSources.scala
@@ -153,6 +153,12 @@ object CrossSources {
 
     val preprocessedInputFromArgs = value(preprocessSources(inputs.flattened()))
 
+    val preprocessedWithUsingDirs =
+      preprocessedInputFromArgs.filter(p => p.options != Some(BuildOptions()) && p.options != None)
+    if (preprocessedWithUsingDirs.length > 1) println(
+      "Warning: using directives detected in multiple files. It is recommended to keep them centralized in the project.scala file."
+    )
+
     val sourcesFromDirectives =
       preprocessedInputFromArgs
         .flatMap(_.options)
diff --git a/modules/integration/src/test/scala/scala/cli/integration/RunTestDefinitions.scala b/modules/integration/src/test/scala/scala/cli/integration/RunTestDefinitions.scala
index b920801fc3..163aa143c2 100644
--- a/modules/integration/src/test/scala/scala/cli/integration/RunTestDefinitions.scala
+++ b/modules/integration/src/test/scala/scala/cli/integration/RunTestDefinitions.scala
@@ -683,6 +683,27 @@ abstract class RunTestDefinitions(val scalaVersionOpt: Option[String])
     }
   }
 
+  test("multiple using directives warning message") {
+    val inputs = TestInputs(
+      os.rel / "Foo.scala" ->
+        s"""//> using scala "3.2.0"
+           |
+           |object Foo extends App {
+           |  println("Foo")
+           |}
+           |""".stripMargin,
+      os.rel / "Bar.scala" -> "",
+      os.rel / "Hello.java" -> "//> using packaging.output \"out\"",
+    )
+    inputs.fromRoot{ root =>
+      val warningMessage = "Warning: using directives detected in multiple files."
+      val output1 = os.proc(TestUtil.cli, ".").call(cwd = root).out.trim()
+      val output2 = os.proc(TestUtil.cli, "Foo.scala", "Bar.scala").call(cwd = root).out.trim()
+      expect(output1.contains(warningMessage))
+      expect(!output2.contains(warningMessage))
+    }
+  }
+
   def sudoTest(): Unit = {
     val fileName = "simple.sc"
     val message  = "Hello"