diff --git a/modules/cli/src/main/scala/scala/cli/commands/run/Run.scala b/modules/cli/src/main/scala/scala/cli/commands/run/Run.scala
index b03b8cbedc..6a87b3c05d 100644
--- a/modules/cli/src/main/scala/scala/cli/commands/run/Run.scala
+++ b/modules/cli/src/main/scala/scala/cli/commands/run/Run.scala
@@ -556,7 +556,7 @@ object Run extends ScalaCommand[RunOptions] with BuildCommandHelpers {
                       )
                   }
                 }
-                process.onExit().thenApply(_ => if os.exists(jsDest) then os.remove(jsDest))
+                process.onExit().thenApply(_ => if os.exists(jsDest) then os.remove.all(jsDest))
                 Right((process, None))
               }
             }
@@ -613,7 +613,9 @@ object Run extends ScalaCommand[RunOptions] with BuildCommandHelpers {
                           esModule = esModule
                         )
                       }
-                      process.onExit().thenApply(_ => if os.exists(jsDest) then os.remove(jsDest))
+                      process.onExit().thenApply(_ =>
+                        if os.exists(jsDest) then os.remove.all(jsDest)
+                      )
                       Right((process, None))
                     }
                   }
@@ -842,7 +844,10 @@ object Run extends ScalaCommand[RunOptions] with BuildCommandHelpers {
         noOpt = noOpt,
         logger = logger
       ).map(outputPath => f(outputPath))
-    finally if os.exists(dest) then os.remove(dest)
+    // `dest` starts as a file, but `linkJs` replaces it with a directory when the linker emits
+    // several files (Wasm, or JS module splitting), so a plain `os.remove` would throw
+    // `DirectoryNotEmptyException` and fail the command after it already succeeded.
+    finally if os.exists(dest) then os.remove.all(dest)
   }
 
   def withNativeLauncher[T](
diff --git a/modules/integration/src/test/scala/scala/cli/integration/TestTestDefinitions.scala b/modules/integration/src/test/scala/scala/cli/integration/TestTestDefinitions.scala
index da821e2d98..31c64af20e 100644
--- a/modules/integration/src/test/scala/scala/cli/integration/TestTestDefinitions.scala
+++ b/modules/integration/src/test/scala/scala/cli/integration/TestTestDefinitions.scala
@@ -377,6 +377,26 @@ abstract class TestTestDefinitions extends ScalaCliSuite with TestScalaVersionAr
     }
   }
 
+  test("successful test Wasm") {
+    successfulTestInputs().fromRoot { root =>
+      // The Wasm backend emits several files (main.js, __loader.js, main.wasm), so the linked
+      // output is a directory: the command must still exit 0 after cleaning it up.
+      val output = os.proc(
+        TestUtil.cli,
+        "--power",
+        "test",
+        extraOptions,
+        ".",
+        "--js-emit-wasm",
+        "--js-module-kind",
+        "es"
+      )
+        .call(cwd = root)
+        .out.text()
+      expect(output.contains("Hello from tests"))
+    }
+  }
+
   test("successful test esmodule import JS") {
     successfulESModuleTestInputs.fromRoot { root =>
       val output = os.proc(TestUtil.cli, "test", extraOptions, ".", "--js")