diff --git a/modules/build/src/main/scala/scala/build/CrossSources.scala b/modules/build/src/main/scala/scala/build/CrossSources.scala
index 05d5afa9c0..bccdfe6e11 100644
--- a/modules/build/src/main/scala/scala/build/CrossSources.scala
+++ b/modules/build/src/main/scala/scala/build/CrossSources.scala
@@ -10,12 +10,13 @@ import scala.build.errors.{
   BuildException,
   CompositeBuildException,
   ExcludeDefinitionError,
-  MalformedDirectiveError
+  MalformedDirectiveError,
+  Severity
 }
 import scala.build.input.ElementsUtils.*
 import scala.build.input.*
 import scala.build.internal.Constants
-import scala.build.internal.util.RegexUtils
+import scala.build.internal.util.{RegexUtils, WarningMessages}
 import scala.build.options.{
   BuildOptions,
   BuildRequirements,
@@ -214,6 +215,9 @@ object CrossSources {
       value(preprocessSources(inputsElemFromDirectives.pipe(elements =>
         value(excludeSources(elements, inputs.workspace, allExclude))
       )))
+
+    warnAboutChainedUsingFileDirectives(preprocessedSourcesFromDirectives, logger)
+
     val allInputs = inputs.add(inputsElemFromDirectives).pipe(inputs =>
       val filteredElements = value(excludeSources(inputs.elements, inputs.workspace, allExclude))
       inputs.withElements(elements = filteredElements)
@@ -462,4 +466,21 @@ object CrossSources {
         ))
     }
   }
+
+  /** When a source file added by a `using file` directive, itself, contains `using file` directives
+    * there should be a warning printed that transitive `using file` directives are not supported.
+    */
+  def warnAboutChainedUsingFileDirectives(
+    sourcesAddedWithDirectives: Seq[PreprocessedSource],
+    logger: Logger
+  ): Unit = for {
+    additionalSource           <- sourcesAddedWithDirectives
+    buildOptions               <- additionalSource.options
+    transitiveAdditionalSource <- buildOptions.internal.extraSourceFiles
+  } do
+    logger.diagnostic(
+      WarningMessages.chainingUsingFileDirective,
+      Severity.Warning,
+      transitiveAdditionalSource.positions
+    )
 }
diff --git a/modules/build/src/main/scala/scala/build/internal/util/WarningMessages.scala b/modules/build/src/main/scala/scala/build/internal/util/WarningMessages.scala
index 49d46916fa..12ce43ebc8 100644
--- a/modules/build/src/main/scala/scala/build/internal/util/WarningMessages.scala
+++ b/modules/build/src/main/scala/scala/build/internal/util/WarningMessages.scala
@@ -95,4 +95,7 @@ object WarningMessages {
       "directive",
       handler.scalaSpecificationLevel
     )
+
+  val chainingUsingFileDirective: String =
+    "Chaining the 'using file' directive is not supported, the source won't be included in the build."
 }
diff --git a/modules/directives/src/main/scala/scala/build/preprocessing/directives/Sources.scala b/modules/directives/src/main/scala/scala/build/preprocessing/directives/Sources.scala
index f3d19f69d0..c382910c5f 100644
--- a/modules/directives/src/main/scala/scala/build/preprocessing/directives/Sources.scala
+++ b/modules/directives/src/main/scala/scala/build/preprocessing/directives/Sources.scala
@@ -18,7 +18,9 @@ import scala.util.Try
     |`//> using files` _path1_ _path2_ …
     |""".stripMargin
 )
-@DirectiveDescription("Manually add sources to the project")
+@DirectiveDescription(
+  "Manually add sources to the project. Does not support chaining, sources are added only once, not recursively."
+)
 @DirectiveLevel(SpecificationLevel.SHOULD)
 // format: off
 final case class Sources(
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 29da426132..84d9717b69 100644
--- a/modules/integration/src/test/scala/scala/cli/integration/RunTestDefinitions.scala
+++ b/modules/integration/src/test/scala/scala/cli/integration/RunTestDefinitions.scala
@@ -1663,7 +1663,7 @@ abstract class RunTestDefinitions(val scalaVersionOpt: Option[String])
   }
 
   // Credentials tests
-  test("Repository credentials passed to coursier") {
+  test("repository credentials passed to coursier") {
     val testOrg     = "test-org"
     val testName    = "the-messages"
     val testVersion = "0.1.2"
@@ -1818,4 +1818,67 @@ abstract class RunTestDefinitions(val scalaVersionOpt: Option[String])
       }
     }
   }
+
+  test("warn about transitive `using file` directive") {
+    TestInputs(
+      os.rel / "Main.scala" ->
+        """//> using file "bar/Bar.scala"
+          |//> using file "abc/Abc.scala"
+          |object Main extends App {
+          | println(Bar(42))
+          |}
+          |""".stripMargin,
+      os.rel / "bar" / "Bar.scala" ->
+        """//> using file "xyz/Xyz.scala"
+          |//> using file "xyz/NonExistent.scala"
+          |case class Bar(x: Int)
+          |""".stripMargin,
+      os.rel / "abc" / "Abc.scala" ->
+        """//> using file "xyz/Xyz.scala"
+          |//> using file "xyz/NonExistent.scala"
+          |case class Abc(x: Int)
+          |""".stripMargin,
+      os.rel / "xyz" / "Xyz.scala" ->
+        """val xyz = 42
+          |""".stripMargin
+    ).fromRoot { root =>
+      val res = os.proc(
+        TestUtil.cli,
+        "compile",
+        "Main.scala",
+        "--suppress-directives-in-multiple-files-warning"
+      )
+        .call(cwd = root, mergeErrIntoOut = true)
+
+      val output = TestUtil.removeAnsiColors(res.out.trim())
+
+      expect(output.contains(
+        """[warn] Chaining the 'using file' directive is not supported, the source won't be included in the build.
+          |[warn] //> using file "xyz/Xyz.scala"
+          |[warn]                 ^^^^^^^^^^^^^
+          |""".stripMargin
+      ))
+
+      expect(output.contains(
+        """[warn] Chaining the 'using file' directive is not supported, the source won't be included in the build.
+          |[warn] //> using file "xyz/NonExistent.scala"
+          |[warn]                 ^^^^^^^^^^^^^^^^^^^^^
+          |""".stripMargin
+      ))
+
+      expect(output.contains(
+        """[warn] Chaining the 'using file' directive is not supported, the source won't be included in the build.
+          |[warn] //> using file "xyz/Xyz.scala"
+          |[warn]                 ^^^^^^^^^^^^^
+          |""".stripMargin
+      ))
+
+      expect(output.contains(
+        """[warn] Chaining the 'using file' directive is not supported, the source won't be included in the build.
+          |[warn] //> using file "xyz/NonExistent.scala"
+          |[warn]                 ^^^^^^^^^^^^^^^^^^^^^
+          |""".stripMargin
+      ))
+    }
+  }
 }
diff --git a/website/docs/reference/directives.md b/website/docs/reference/directives.md
index 330b7d8be4..fb87de1706 100644
--- a/website/docs/reference/directives.md
+++ b/website/docs/reference/directives.md
@@ -73,7 +73,7 @@ Manually add JAR(s) to the class path
 
 ### Custom sources
 
-Manually add sources to the project
+Manually add sources to the project. Does not support chaining, sources are added only once, not recursively.
 
 `//> using file` _path_
 
diff --git a/website/docs/reference/scala-command/directives.md b/website/docs/reference/scala-command/directives.md
index 1bd0cc1c50..f31934b9f9 100644
--- a/website/docs/reference/scala-command/directives.md
+++ b/website/docs/reference/scala-command/directives.md
@@ -123,7 +123,7 @@ Manually add JAR(s) to the class path
 
 ### Custom sources
 
-Manually add sources to the project
+Manually add sources to the project. Does not support chaining, sources are added only once, not recursively.
 
 `//> using file` _path_