diff --git a/rust/private/rust.bzl b/rust/private/rust.bzl
index 88b98d1e60..d6f09e855e 100644
--- a/rust/private/rust.bzl
+++ b/rust/private/rust.bzl
@@ -251,15 +251,16 @@ def _rust_library_common(ctx, crate_type):
     Returns:
         list: A list of providers. See `rustc_compile_action`
     """
-
-    srcs, crate_root = _transform_sources(ctx, ctx.files.srcs, getattr(ctx.file, "crate_root", None))
-    if not crate_root:
-        crate_root = crate_root_src(ctx.attr.name, srcs, "lib")
     _assert_no_deprecated_attributes(ctx)
     _assert_correct_dep_mapping(ctx)
 
     toolchain = find_toolchain(ctx)
 
+    crate_root = getattr(ctx.file, "crate_root", None)
+    if not crate_root:
+        crate_root = crate_root_src(ctx.attr.name, ctx.files.srcs, crate_type)
+    srcs, crate_root = _transform_sources(ctx, ctx.files.srcs, crate_root)
+
     # Determine unique hash for this rlib.
     # Note that we don't include a hash for `cdylib` and `staticlib` since they are meant to be consumed externally
     # and having a deterministic name is important since it ends up embedded in the executable. This is problematic
@@ -332,9 +333,10 @@ def _rust_binary_impl(ctx):
     deps = transform_deps(ctx.attr.deps)
     proc_macro_deps = transform_deps(ctx.attr.proc_macro_deps + get_import_macro_deps(ctx))
 
-    srcs, crate_root = _transform_sources(ctx, ctx.files.srcs, getattr(ctx.file, "crate_root", None))
+    crate_root = getattr(ctx.file, "crate_root", None)
     if not crate_root:
-        crate_root = crate_root_src(ctx.attr.name, srcs, ctx.attr.crate_type)
+        crate_root = crate_root_src(ctx.attr.name, ctx.files.srcs, ctx.attr.crate_type)
+    srcs, crate_root = _transform_sources(ctx, ctx.files.srcs, crate_root)
 
     return rustc_compile_action(
         ctx = ctx,
@@ -373,9 +375,7 @@ def _rust_test_impl(ctx):
 
     toolchain = find_toolchain(ctx)
 
-    srcs, crate_root = _transform_sources(ctx, ctx.files.srcs, getattr(ctx.file, "crate_root", None))
     crate_type = "bin"
-
     deps = transform_deps(ctx.attr.deps)
     proc_macro_deps = transform_deps(ctx.attr.proc_macro_deps + get_import_macro_deps(ctx))
 
@@ -392,6 +392,8 @@ def _rust_test_impl(ctx):
             ),
         )
 
+        srcs, crate_root = _transform_sources(ctx, ctx.files.srcs, getattr(ctx.file, "crate_root", None))
+
         # Optionally join compile data
         if crate.compile_data:
             compile_data = depset(ctx.files.compile_data, transitive = [crate.compile_data])
@@ -425,9 +427,12 @@ def _rust_test_impl(ctx):
             owner = ctx.label,
         )
     else:
+        crate_root = getattr(ctx.file, "crate_root", None)
+
         if not crate_root:
             crate_root_type = "lib" if ctx.attr.use_libtest_harness else "bin"
             crate_root = crate_root_src(ctx.attr.name, ctx.files.srcs, crate_root_type)
+        srcs, crate_root = _transform_sources(ctx, ctx.files.srcs, crate_root)
 
         output_hash = determine_output_hash(crate_root, ctx.label)
         output = ctx.actions.declare_file(
diff --git a/test/generated_inputs/BUILD.bazel b/test/generated_inputs/BUILD.bazel
index 19fc8e6f66..646f019394 100644
--- a/test/generated_inputs/BUILD.bazel
+++ b/test/generated_inputs/BUILD.bazel
@@ -84,6 +84,17 @@ rust_library(
     tags = ["norustfmt"],
 )
 
+rust_test(
+    name = "use_generated_src_with_crate_root_in_subdir_srcs_test",
+    srcs = [
+        "src/generated.rs",
+        "src/generated/submodule.rs",
+        "src/lib.rs",
+    ],
+    edition = "2018",
+    tags = ["norustfmt"],
+)
+
 rust_test(
     name = "use_generated_src_with_crate_root_in_subdir_test",
     crate = "use_generated_src_with_crate_root_in_subdir",