diff --git a/src/cargo/core/compiler/build_runner/compilation_files.rs b/src/cargo/core/compiler/build_runner/compilation_files.rs
index 46329f947cd..8cb56d22adb 100644
--- a/src/cargo/core/compiler/build_runner/compilation_files.rs
+++ b/src/cargo/core/compiler/build_runner/compilation_files.rs
@@ -449,7 +449,13 @@ impl<'a, 'gctx: 'a> CompilationFiles<'a, 'gctx> {
     ///
     /// Returns `None` if the unit shouldn't be uplifted (for example, a
     /// dependent rlib).
-    fn uplift_to(&self, unit: &Unit, file_type: &FileType, from_path: &Path) -> Option<PathBuf> {
+    fn uplift_to(
+        &self,
+        unit: &Unit,
+        file_type: &FileType,
+        from_path: &Path,
+        bcx: &BuildContext<'_, '_>,
+    ) -> Option<PathBuf> {
         // Tests, check, doc, etc. should not be uplifted.
         if unit.mode != CompileMode::Build || file_type.flavor == FileFlavor::Rmeta {
             return None;
@@ -460,6 +466,11 @@ impl<'a, 'gctx: 'a> CompilationFiles<'a, 'gctx> {
             return None;
         }
 
+        // Build script bins are never uplifted.
+        if bcx.gctx.cli_unstable().build_dir_new_layout && unit.target.is_custom_build() {
+            return None;
+        }
+
         // - Binaries: The user always wants to see these, even if they are
         //   implicitly built (for example for integration tests).
         // - dylibs: This ensures that the dynamic linker pulls in all the
@@ -645,7 +656,7 @@ impl<'a, 'gctx: 'a> CompilationFiles<'a, 'gctx> {
 
             // If, the `different_binary_name` feature is enabled, the name of the hardlink will
             // be the name of the binary provided by the user in `Cargo.toml`.
-            let hardlink = self.uplift_to(unit, &file_type, &path);
+            let hardlink = self.uplift_to(unit, &file_type, &path, bcx);
             let export_path = if unit.target.is_custom_build() {
                 None
             } else {
@@ -905,8 +916,8 @@ fn use_extra_filename(bcx: &BuildContext<'_, '_>, unit: &Unit) -> bool {
         }
         // No metadata in these cases:
         //
-        // - dylib, cdylib, executable: `pkg_dir` avoids collisions for us and rustc isn't looking these
-        //   up by `-Cextra-filename`
+        // - dylib, cdylib, executable, build-scripts: `pkg_dir` avoids collisions for us and rustc isn't
+        // looking these up by `-Cextra-filename`
         //
         // The __CARGO_DEFAULT_LIB_METADATA env var is used to override this to
         // force metadata in the hash. This is only used for building libstd. For
@@ -915,7 +926,10 @@ fn use_extra_filename(bcx: &BuildContext<'_, '_>, unit: &Unit) -> bool {
         // installs. In addition it prevents accidentally loading a libstd of a
         // different compiler at runtime.
         // See https://github.com/rust-lang/cargo/issues/3005
-        if (unit.target.is_dylib() || unit.target.is_cdylib() || unit.target.is_executable())
+        if (unit.target.is_dylib()
+            || unit.target.is_cdylib()
+            || unit.target.is_executable()
+            || unit.target.is_custom_build())
             && bcx.gctx.get_env("__CARGO_DEFAULT_LIB_METADATA").is_err()
         {
             return false;
diff --git a/src/cargo/core/compiler/custom_build.rs b/src/cargo/core/compiler/custom_build.rs
index 1cd4c994faf..f4f77b70950 100644
--- a/src/cargo/core/compiler/custom_build.rs
+++ b/src/cargo/core/compiler/custom_build.rs
@@ -349,7 +349,12 @@ fn build_work(build_runner: &mut BuildRunner<'_, '_>, unit: &Unit) -> CargoResul
     }
 
     // Building the command to execute
-    let to_exec = script_dir.join(unit.target.name());
+    let bin_name = if bcx.gctx.cli_unstable().build_dir_new_layout {
+        unit.target.crate_name()
+    } else {
+        unit.target.name().to_string()
+    };
+    let to_exec = script_dir.join(bin_name);
 
     // Start preparing the process to execute, starting out with some
     // environment variables. Note that the profile-related environment
diff --git a/tests/testsuite/build_dir.rs b/tests/testsuite/build_dir.rs
index d1ce0b828b9..0d4b88084b0 100644
--- a/tests/testsuite/build_dir.rs
+++ b/tests/testsuite/build_dir.rs
@@ -281,9 +281,8 @@ fn build_script_should_output_to_build_dir() {
 [ROOT]/foo/build-dir/CACHEDIR.TAG
 [ROOT]/foo/build-dir/debug/.cargo-build-lock
 [ROOT]/foo/build-dir/debug/build/foo/[HASH]/out/foo.txt
-[ROOT]/foo/build-dir/debug/build/foo/[HASH]/out/build_script_build[..].d
-[ROOT]/foo/build-dir/debug/build/foo/[HASH]/out/build_script_build[..][EXE]
-[ROOT]/foo/build-dir/debug/build/foo/[HASH]/out/build-script-build[EXE]
+[ROOT]/foo/build-dir/debug/build/foo/[HASH]/out/build_script_build.d
+[ROOT]/foo/build-dir/debug/build/foo/[HASH]/out/build_script_build[EXE]
 [ROOT]/foo/build-dir/debug/build/foo/[HASH]/out/foo[..][EXE]
 [ROOT]/foo/build-dir/debug/build/foo/[HASH]/out/foo[..].d
 [ROOT]/foo/build-dir/debug/build/foo/[HASH]/fingerprint/invoked.timestamp
diff --git a/tests/testsuite/clean_new_layout.rs b/tests/testsuite/clean_new_layout.rs
index de0e7c6f288..b69ecc23497 100644
--- a/tests/testsuite/clean_new_layout.rs
+++ b/tests/testsuite/clean_new_layout.rs
@@ -401,7 +401,7 @@ fn build_script() {
         .with_stderr_data(str![[r#"
 [COMPILING] foo v0.0.1 ([ROOT]/foo)
 [RUNNING] `rustc [..] build.rs [..]`
-[RUNNING] `[ROOT]/foo/target/debug/build/foo/[HASH]/out/build-script-build`
+[RUNNING] `[ROOT]/foo/target/debug/build/foo/[HASH]/out/build_script_build`
 [RUNNING] `rustc [..] src/main.rs [..]`
 [FINISHED] `dev` profile [unoptimized + debuginfo] target(s) in [ELAPSED]s