diff --git a/src/cargo/core/compiler/build_runner/compilation_files.rs b/src/cargo/core/compiler/build_runner/compilation_files.rs
index f09e591bd33..f6817a60a85 100644
--- a/src/cargo/core/compiler/build_runner/compilation_files.rs
+++ b/src/cargo/core/compiler/build_runner/compilation_files.rs
@@ -220,7 +220,7 @@ impl<'a, 'gctx: 'a> CompilationFiles<'a, 'gctx> {
             panic!("doc tests do not have an out dir");
         } else if unit.target.is_custom_build() {
             self.build_script_dir(unit)
-        } else if unit.target.is_example() {
+        } else if unit.target.is_example() && !self.ws.gctx().cli_unstable().build_dir_new_layout {
             self.layout(unit.kind).build_dir().examples().to_path_buf()
         } else if unit.artifact.is_true() {
             self.artifact_dir(unit)
diff --git a/src/cargo/ops/cargo_clean.rs b/src/cargo/ops/cargo_clean.rs
index 37f205c6250..dd4c3993fc1 100644
--- a/src/cargo/ops/cargo_clean.rs
+++ b/src/cargo/ops/cargo_clean.rs
@@ -209,6 +209,7 @@ fn clean_specs(
                 if target.is_custom_build() {
                     continue;
                 }
+                let crate_name: Rc<str> = target.crate_name().into();
                 for &mode in &[
                     CompileMode::Build,
                     CompileMode::Test,
@@ -240,6 +241,10 @@ fn clean_specs(
                                 clean_ctx.rm_rf(&dep_info)?;
                             }
                         }
+
+                        let dir = escape_glob_path(layout.build_dir().incremental())?;
+                        let incremental = Path::new(&dir).join(format!("{}-*", crate_name));
+                        clean_ctx.rm_rf_glob(&incremental)?;
                     }
                 }
             }
diff --git a/tests/testsuite/build_dir.rs b/tests/testsuite/build_dir.rs
index 8e409bcf932..d2b7ebf4260 100644
--- a/tests/testsuite/build_dir.rs
+++ b/tests/testsuite/build_dir.rs
@@ -396,8 +396,8 @@ fn examples_should_output_to_build_dir_and_uplift_to_target_dir() {
 [ROOT]/foo/build-dir/debug/build/foo/[HASH]/fingerprint/example-foo
 [ROOT]/foo/build-dir/debug/build/foo/[HASH]/fingerprint/example-foo.json
 [ROOT]/foo/build-dir/debug/build/foo/[HASH]/fingerprint/invoked.timestamp
-[ROOT]/foo/build-dir/debug/examples/foo[..][EXE]
-[ROOT]/foo/build-dir/debug/examples/foo[..].d
+[ROOT]/foo/build-dir/debug/build/foo/[HASH]/deps/foo[..][EXE]
+[ROOT]/foo/build-dir/debug/build/foo/[HASH]/deps/foo[..].d
 
 "#]]);
 
diff --git a/tests/testsuite/clean_new_layout.rs b/tests/testsuite/clean_new_layout.rs
index 33d618fabec..ad4b01c982b 100644
--- a/tests/testsuite/clean_new_layout.rs
+++ b/tests/testsuite/clean_new_layout.rs
@@ -142,6 +142,10 @@ fn clean_multiple_packages_in_glob_char_path() {
     p.cargo("clean -p foo")
         .arg("-Zbuild-dir-new-layout")
         .masquerade_as_nightly_cargo(&["new build-dir layout"])
+        .with_stderr_data(str![[r#"
+[REMOVED] [FILE_NUM] files, [FILE_SIZE]B total
+
+"#]])
         .run();
     assert_eq!(get_build_artifacts(foo_path, file_glob).len(), 0);
 }
@@ -598,7 +602,7 @@ fn package_cleans_all_the_things() {
             .arg("-Zbuild-dir-new-layout")
             .masquerade_as_nightly_cargo(&["new build-dir layout"])
             .run();
-        //assert_all_clean(&p.build_dir());  // FIXME
+        assert_all_clean(&p.build_dir());
     }
     let p = project()
         .file(
@@ -657,7 +661,7 @@ fn package_cleans_all_the_things() {
         .arg("-Zbuild-dir-new-layout")
         .masquerade_as_nightly_cargo(&["new build-dir layout"])
         .run();
-    //assert_all_clean(&p.build_dir());  // FIXME
+    assert_all_clean(&p.build_dir());
 
     // Try some targets.
     p.cargo("build --all-targets --target")
@@ -670,7 +674,43 @@ fn package_cleans_all_the_things() {
         .arg("-Zbuild-dir-new-layout")
         .masquerade_as_nightly_cargo(&["new build-dir layout"])
         .run();
-    //assert_all_clean(&p.build_dir());  // FIXME
+    assert_all_clean(&p.build_dir());
+}
+
+// Ensures that all files for the package have been deleted.
+#[track_caller]
+fn assert_all_clean(build_dir: &Path) {
+    let walker = walkdir::WalkDir::new(build_dir).into_iter();
+    for entry in walker.filter_entry(|e| {
+        let path = e.path();
+        // This is a known limitation, clean can't differentiate between
+        // the different build scripts from different packages.
+        !(path
+            .file_name()
+            .unwrap()
+            .to_str()
+            .unwrap()
+            .starts_with("build_script_build")
+            && path
+                .parent()
+                .unwrap()
+                .file_name()
+                .unwrap()
+                .to_str()
+                .unwrap()
+                == "incremental")
+    }) {
+        let entry = entry.unwrap();
+        let path = entry.path();
+        if let ".rustc_info.json" | ".cargo-lock" | "CACHEDIR.TAG" =
+            path.file_name().unwrap().to_str().unwrap()
+        {
+            continue;
+        }
+        if path.is_symlink() || path.is_file() {
+            panic!("{:?} was not cleaned", path);
+        }
+    }
 }
 
 #[cargo_test]