diff --git a/toolchain/internal/configure.bzl b/toolchain/internal/configure.bzl
index 16afd5f8..acc5135e 100644
--- a/toolchain/internal/configure.bzl
+++ b/toolchain/internal/configure.bzl
@@ -314,7 +314,7 @@ def _cc_toolchain_str(
     # visible via the "built_in_include_directories" attribute of CcToolchainInfo as well as to keep
     # them in sync with the directories included in the system module map generated for the stricter
     # "layering_check" feature.
-    toolchain_path_prefix = toolchain_info.llvm_dist_path_prefix
+    toolchain_path_prefix = "%workspace%/" + toolchain_info.llvm_dist_path_prefix
     llvm_version = toolchain_info.llvm_version
     major_llvm_version = int(llvm_version.split(".")[0])
     target_system_name = {
diff --git a/toolchain/internal/system_module_map.bzl b/toolchain/internal/system_module_map.bzl
index 992952e4..92571fd9 100644
--- a/toolchain/internal/system_module_map.bzl
+++ b/toolchain/internal/system_module_map.bzl
@@ -37,6 +37,8 @@ def _system_module_map(ctx):
     for include_dir in ctx.attr.cxx_builtin_include_directories:
         if ctx.attr.sysroot_path and include_dir.startswith("%sysroot%"):
             include_dir = ctx.attr.sysroot_path + include_dir[len("%sysroot%"):]
+        if include_dir.startswith("%workspace%/"):
+            include_dir = include_dir.removeprefix("%workspace%/")
         include_dir = paths.normalize(include_dir).replace("//", "/")
         if include_dir.startswith("/"):
             absolute_path_dirs.append(include_dir)