diff --git a/modules/build/src/main/scala/scala/build/CrossSources.scala b/modules/build/src/main/scala/scala/build/CrossSources.scala
index 362ad844ba..69cb83f7a0 100644
--- a/modules/build/src/main/scala/scala/build/CrossSources.scala
+++ b/modules/build/src/main/scala/scala/build/CrossSources.scala
@@ -153,6 +153,29 @@ object CrossSources {
 
     val preprocessedInputFromArgs = value(preprocessSources(inputs.flattened()))
 
+    val preprocessedWithUsingDirs =
+      preprocessedInputFromArgs.filter(p => p.options.exists(_ != BuildOptions.monoid.zero))
+
+    if (preprocessedWithUsingDirs.length > 1)
+      val projectFilePath = inputs.elements.projectSettingsFiles.headOption match
+        case Some(s) => s.path
+        case _       => inputs.workspace / "project.scala"
+
+      preprocessedWithUsingDirs
+        .filter(p => os.Path(p.scopePath.path, os.root) != projectFilePath)
+        .foreach { file =>
+          file.scopePath.root match
+            case Right(base: os.Path) =>
+              val path = os.Path(file.scopePath.path, base)
+              val linesNumbers = os.read.lines(path).zipWithIndex
+                .filter((ln, _) => ln.startsWith("//> using"))
+                .map((_, idx) => idx + 1)
+              logger.diagnostic(
+                s"WARNING: using directives detected in $path [Ln: ${linesNumbers.mkString(", ")}]. It is recommended to keep them centralized in the $projectFilePath file."
+              )
+            case _ => ()
+        }
+
     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..82e14f073b 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 +683,30 @@ 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"
+      val output1        = os.proc(TestUtil.cli, ".").call(cwd = root, stderr = os.Pipe).err.trim()
+      val output2 = os.proc(TestUtil.cli, "Foo.scala", "Bar.scala").call(
+        cwd = root,
+        stderr = os.Pipe
+      ).err.trim()
+      expect(output1.contains(warningMessage))
+      expect(!output2.contains(warningMessage))
+    }
+  }
+
   def sudoTest(): Unit = {
     val fileName = "simple.sc"
     val message  = "Hello"