diff --git a/src/cargo/core/compiler/custom_build.rs b/src/cargo/core/compiler/custom_build.rs
index be04dbe304c..a96d2cdeed0 100644
--- a/src/cargo/core/compiler/custom_build.rs
+++ b/src/cargo/core/compiler/custom_build.rs
@@ -343,7 +343,6 @@ fn build_work(build_runner: &mut BuildRunner<'_, '_>, unit: &Unit) -> CargoResul
     } else {
         build_runner.files().build_script_out_dir(unit)
     };
-    let script_run_dir = build_runner.files().build_script_run_dir(unit);
 
     if let Some(deps) = unit.pkg.manifest().metabuild() {
         prepare_metabuild(build_runner, build_script_unit, deps)?;
@@ -490,16 +489,14 @@ fn build_work(build_runner: &mut BuildRunner<'_, '_>, unit: &Unit) -> CargoResul
     let pkg_descr = unit.pkg.to_string();
     let build_script_outputs = Arc::clone(&build_runner.build_script_outputs);
     let id = unit.pkg.package_id();
-    let output_file = script_run_dir.join("output");
-    let err_file = script_run_dir.join("stderr");
-    let root_output_file = script_run_dir.join("root-output");
+    let run_files = BuildScriptRunFiles::for_unit(build_runner, unit);
     let host_target_root = build_runner.files().host_dest().map(|v| v.to_path_buf());
     let all = (
         id,
         library_name.clone(),
         pkg_descr.clone(),
         Arc::clone(&build_script_outputs),
-        output_file.clone(),
+        run_files.stdout.clone(),
         script_out_dir.clone(),
     );
     let build_scripts = build_runner.build_scripts.get(unit).cloned();
@@ -510,7 +507,7 @@ fn build_work(build_runner: &mut BuildRunner<'_, '_>, unit: &Unit) -> CargoResul
 
     paths::create_dir_all(&script_dir)?;
     paths::create_dir_all(&script_out_dir)?;
-    paths::create_dir_all(&script_run_dir)?;
+    paths::create_dir_all(&run_files.root)?;
 
     let nightly_features_allowed = build_runner.bcx.gctx.nightly_features_allowed;
     let targets: Vec<Target> = unit.pkg.targets().to_vec();
@@ -584,7 +581,7 @@ fn build_work(build_runner: &mut BuildRunner<'_, '_>, unit: &Unit) -> CargoResul
 
         // And now finally, run the build command itself!
         state.running(&cmd);
-        let timestamp = paths::set_invocation_time(&script_run_dir)?;
+        let timestamp = paths::set_invocation_time(&run_files.root)?;
         let prefix = format!("[{} {}] ", id.name(), id.version());
         let mut log_messages_in_case_of_panic = Vec::new();
         let span = tracing::debug_span!("build_script", process = cmd.to_string());
@@ -669,12 +666,12 @@ fn build_work(build_runner: &mut BuildRunner<'_, '_>, unit: &Unit) -> CargoResul
         // This is also the location where we provide feedback into the build
         // state informing what variables were discovered via our script as
         // well.
-        paths::write(&output_file, &output.stdout)?;
+        paths::write(&run_files.stdout, &output.stdout)?;
         // This mtime shift allows Cargo to detect if a source file was
         // modified in the middle of the build.
-        paths::set_file_time_no_err(output_file, timestamp);
-        paths::write(&err_file, &output.stderr)?;
-        paths::write(&root_output_file, paths::path2bytes(&script_out_dir)?)?;
+        paths::set_file_time_no_err(run_files.stdout, timestamp);
+        paths::write(&run_files.stderr, &output.stderr)?;
+        paths::write(&run_files.root_output, paths::path2bytes(&script_out_dir)?)?;
         let parsed_output = BuildOutput::parse(
             &output.stdout,
             library_name,
@@ -1355,10 +1352,9 @@ pub fn build_map(build_runner: &mut BuildRunner<'_, '_>) -> CargoResult<()> {
 
     /// Load any dependency declarations from a previous build script run.
     fn parse_previous_explicit_deps(build_runner: &mut BuildRunner<'_, '_>, unit: &Unit) {
-        let script_run_dir = build_runner.files().build_script_run_dir(unit);
-        let output_file = script_run_dir.join("output");
+        let run_files = BuildScriptRunFiles::for_unit(build_runner, unit);
         let (prev_output, _) = prev_build_output(build_runner, unit);
-        let deps = BuildDeps::new(&output_file, prev_output.as_ref());
+        let deps = BuildDeps::new(&run_files.stdout, prev_output.as_ref());
         build_runner.build_explicit_deps.insert(unit.clone(), deps);
     }
 }
@@ -1377,17 +1373,15 @@ fn prev_build_output(
     } else {
         build_runner.files().build_script_out_dir(unit)
     };
-    let script_run_dir = build_runner.files().build_script_run_dir(unit);
-    let root_output_file = script_run_dir.join("root-output");
-    let output_file = script_run_dir.join("output");
+    let run_files = BuildScriptRunFiles::for_unit(build_runner, unit);
 
-    let prev_script_out_dir = paths::read_bytes(&root_output_file)
+    let prev_script_out_dir = paths::read_bytes(&run_files.root_output)
         .and_then(|bytes| paths::bytes2path(&bytes))
         .unwrap_or_else(|_| script_out_dir.clone());
 
     (
         BuildOutput::parse_file(
-            &output_file,
+            &run_files.stdout,
             unit.pkg.library().map(|t| t.crate_name()),
             &unit.pkg.to_string(),
             &prev_script_out_dir,
@@ -1434,3 +1428,35 @@ impl BuildScriptOutputs {
         self.outputs.iter()
     }
 }
+
+/// Files with information about a running build script.
+struct BuildScriptRunFiles {
+    /// The directory containing files related to running a build script.
+    root: PathBuf,
+    /// The stdout produced by the build script
+    stdout: PathBuf,
+    /// The stderr produced by the build script
+    stderr: PathBuf,
+    /// A file that contains the path of `root`.
+    /// This is used for detect if the directory was moved since the previous run.
+    root_output: PathBuf,
+}
+
+impl BuildScriptRunFiles {
+    pub fn for_unit(build_runner: &BuildRunner<'_, '_>, unit: &Unit) -> Self {
+        let root = build_runner.files().build_script_run_dir(unit);
+        let stdout = if build_runner.bcx.gctx.cli_unstable().build_dir_new_layout {
+            root.join("stdout")
+        } else {
+            root.join("output")
+        };
+        let stderr = root.join("stderr");
+        let root_output = root.join("root-output");
+        Self {
+            root,
+            stdout,
+            stderr,
+            root_output,
+        }
+    }
+}
diff --git a/tests/testsuite/build_dir.rs b/tests/testsuite/build_dir.rs
index 60bd27a5171..92f17e7b5dd 100644
--- a/tests/testsuite/build_dir.rs
+++ b/tests/testsuite/build_dir.rs
@@ -297,7 +297,7 @@ fn build_script_should_output_to_build_dir() {
 [ROOT]/foo/build-dir/debug/build/foo/[HASH]/fingerprint/build-script-build-script-build
 [ROOT]/foo/build-dir/debug/build/foo/[HASH]/fingerprint/build-script-build-script-build.json
 [ROOT]/foo/build-dir/debug/build/foo/[HASH]/run/invoked.timestamp
-[ROOT]/foo/build-dir/debug/build/foo/[HASH]/run/output
+[ROOT]/foo/build-dir/debug/build/foo/[HASH]/run/stdout
 [ROOT]/foo/build-dir/debug/build/foo/[HASH]/run/root-output
 [ROOT]/foo/build-dir/debug/build/foo/[HASH]/run/stderr
 [ROOT]/foo/build-dir/debug/build/foo/[HASH]/.lock