diff --git a/modules/build/src/main/scala/scala/build/CrossSources.scala b/modules/build/src/main/scala/scala/build/CrossSources.scala
index f9c917d49b..c7e731752a 100644
--- a/modules/build/src/main/scala/scala/build/CrossSources.scala
+++ b/modules/build/src/main/scala/scala/build/CrossSources.scala
@@ -273,8 +273,19 @@ object CrossSources {
       )
     }).flatten
 
+    val resourceDirectoriesFromDirectives = {
+      val resourceDirsFromCli =
+        allInputs.elements.flatMap { case rd: ResourceDirectory => Some(rd.path); case _ => None }
+      val resourceDirsFromBuildOptions: Seq[os.Path] =
+        buildOptions.flatMap(_.value.classPathOptions.resourcesDir).distinct
+      resourceDirsFromBuildOptions
+        .filter(!resourceDirsFromCli.contains(_))
+        .map(ResourceDirectory(_))
+    }
+    val finalInputs = allInputs.add(resourceDirectoriesFromDirectives)
+
     val defaultMainElemPath = for {
-      defaultMainElem <- allInputs.defaultMainClassElement
+      defaultMainElem <- finalInputs.defaultMainClassElement
     } yield defaultMainElem.path
 
     val pathsWithDirectivePositions
@@ -284,7 +295,7 @@ object CrossSources {
           val baseReqs0 = baseReqs(d.scopePath)
           WithBuildRequirements(
             d.requirements.fold(baseReqs0)(_ orElse baseReqs0),
-            (d.path, d.path.relativeTo(allInputs.workspace))
+            (d.path, d.path.relativeTo(finalInputs.workspace))
           ) -> d.directivesPositions
       }
     val inMemoryWithDirectivePositions
@@ -309,7 +320,7 @@ object CrossSources {
       }
 
     val resourceDirs: Seq[WithBuildRequirements[os.Path]] =
-      resolveResourceDirs(allInputs, preprocessedSources)
+      resolveResourceDirs(finalInputs, preprocessedSources)
 
     lazy val allPathsWithDirectivesByScope: Map[Scope, Seq[(os.Path, Position.File)]] =
       (pathsWithDirectivePositions ++ inMemoryWithDirectivePositions ++ unwrappedScriptsWithDirectivePositions)
@@ -362,17 +373,15 @@ object CrossSources {
     val paths            = pathsWithDirectivePositions.map(_._1)
     val inMemory         = inMemoryWithDirectivePositions.map(_._1)
     val unwrappedScripts = unwrappedScriptsWithDirectivePositions.map(_._1)
-    (
-      CrossSources(
-        paths,
-        inMemory,
-        defaultMainElemPath,
-        resourceDirs,
-        buildOptions,
-        unwrappedScripts
-      ),
-      allInputs
+    val crossSources = CrossSources(
+      paths,
+      inMemory,
+      defaultMainElemPath,
+      resourceDirs,
+      buildOptions,
+      unwrappedScripts
     )
+    crossSources -> finalInputs
   }
 
   /** @return
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 61ccd1e5ed..47423da68c 100644
--- a/modules/integration/src/test/scala/scala/cli/integration/RunTestDefinitions.scala
+++ b/modules/integration/src/test/scala/scala/cli/integration/RunTestDefinitions.scala
@@ -560,8 +560,10 @@ abstract class RunTestDefinitions
       forbiddenDirTest()
     }
 
-  private def resourcesInputs(directive: String = "") = {
-    val resourceContent = "Hello from resources"
+  protected def resourcesInputs(
+    directive: String = "",
+    resourceContent: String = "Hello from resources"
+  ): TestInputs =
     TestInputs(
       os.rel / "src" / "proj" / "resources" / "test" / "data" -> resourceContent,
       os.rel / "src" / "proj" / "Test.scala" ->
@@ -571,24 +573,30 @@ abstract class RunTestDefinitions
            |    val cl = Thread.currentThread().getContextClassLoader
            |    val is = cl.getResourceAsStream("test/data")
            |    val content = scala.io.Source.fromInputStream(is)(scala.io.Codec.UTF8).mkString
-           |    assert(content == "$resourceContent")
+           |    println(content)
            |  }
            |}
            |""".stripMargin
     )
-  }
 
-  test("resources") {
-    resourcesInputs().fromRoot { root =>
-      os.proc(TestUtil.cli, "run", "src", "--resource-dirs", "./src/proj/resources").call(cwd =
-        root
-      )
+  test("resources via command line") {
+    val expectedMessage = "hello"
+    resourcesInputs(resourceContent = expectedMessage).fromRoot { root =>
+      val res = os.proc(TestUtil.cli, "run", "src", "--resource-dirs", "./src/proj/resources")
+        .call(cwd = root)
+      expect(res.out.trim() == expectedMessage)
     }
   }
   test("resources via directive") {
-    resourcesInputs("//> using resourceDirs \"./resources\"").fromRoot { root =>
-      os.proc(TestUtil.cli, "run", ".").call(cwd = root)
-    }
+    val expectedMessage = "hello"
+    resourcesInputs(
+      directive = "//> using resourceDirs \"./resources\"",
+      resourceContent = expectedMessage
+    )
+      .fromRoot { root =>
+        val res = os.proc(TestUtil.cli, "run", ".").call(cwd = root)
+        expect(res.out.trim() == expectedMessage)
+      }
   }
 
   def argsAsIsTest(): Unit = {
diff --git a/modules/integration/src/test/scala/scala/cli/integration/RunWithWatchTestDefinitions.scala b/modules/integration/src/test/scala/scala/cli/integration/RunWithWatchTestDefinitions.scala
index 6021aa3e9e..5034c06932 100644
--- a/modules/integration/src/test/scala/scala/cli/integration/RunWithWatchTestDefinitions.scala
+++ b/modules/integration/src/test/scala/scala/cli/integration/RunWithWatchTestDefinitions.scala
@@ -42,6 +42,18 @@ trait RunWithWatchTestDefinitions { _: RunTestDefinitions =>
               TestInputs(inputPath -> code(expectedMessage1)),
               code(expectedMessage2)
             )
+          }, {
+            val inputPath = os.rel / "Main.java"
+            def code(message: String) = s"""public class Main {
+                                           |  public static void main(String[] args) {
+                                           |    System.out.println("$message");
+                                           |  }
+                                           |}""".stripMargin
+            (
+              inputPath,
+              TestInputs(inputPath -> code(expectedMessage1)),
+              code(expectedMessage2)
+            )
           }, {
             val inputPath = os.rel / "markdown.md"
             def code(message: String) =
@@ -296,4 +308,34 @@ trait RunWithWatchTestDefinitions { _: RunTestDefinitions =>
         }
       }
     }
+
+  for {
+    useDirective <- Seq(false, true)
+    // TODO make this pass reliably on Mac CI
+    if !Properties.isMac || !TestUtil.isCI
+    directive       = if (useDirective) "//> using resourceDirs ./resources" else ""
+    resourceOptions = if (useDirective) Nil else Seq("--resource-dirs", "./src/proj/resources")
+    title           = if (useDirective) "directive" else "command line"
+  } test(s"resources via $title with --watch") {
+    val expectedMessage1 = "Hello"
+    val expectedMessage2 = "world"
+    resourcesInputs(directive = directive, resourceContent = expectedMessage1)
+      .fromRoot { root =>
+        TestUtil.withProcessWatching(
+          os.proc(TestUtil.cli, "run", "src", "--watch", resourceOptions, extraOptions)
+            .spawn(cwd = root, stderr = os.Pipe)
+        ) { (proc, timeout, ec) =>
+          val output1 = TestUtil.readLine(proc.stdout, ec, timeout)
+          expect(output1 == expectedMessage1)
+          proc.printStderrUntilRerun(timeout)(ec)
+          val Some((resourcePath, newResourceContent)) =
+            resourcesInputs(directive = directive, resourceContent = expectedMessage2)
+              .files
+              .find(_._1.toString.contains("resources"))
+          os.write.over(root / resourcePath, newResourceContent)
+          val output2 = TestUtil.readLine(proc.stdout, ec, timeout)
+          expect(output2 == expectedMessage2)
+        }
+      }
+  }
 }