diff --git a/cargo/private/cargo_build_script.bzl b/cargo/private/cargo_build_script.bzl
index be08907ebe..d376b31301 100644
--- a/cargo/private/cargo_build_script.bzl
+++ b/cargo/private/cargo_build_script.bzl
@@ -153,7 +153,7 @@ def get_cc_compile_args_and_env(cc_toolchain, feature_configuration):
     )
     return cc_c_args, cc_cxx_args, cc_env
 
-def _pwd_flags_sysroot(args):
+def _pwd_flags(args):
     """Prefix execroot-relative paths of known arguments with ${pwd}.
 
     Args:
@@ -163,56 +163,33 @@ def _pwd_flags_sysroot(args):
         list: The modified argument list.
     """
     res = []
-    for arg in args:
-        s, opt, path = arg.partition("--sysroot=")
-        if s == "" and not paths.is_absolute(path):
-            res.append("{}${{pwd}}/{}".format(opt, path))
-        else:
-            res.append(arg)
-    return res
+    fix_next_arg = False
 
-def _pwd_flags_isystem(args):
-    """Prefix execroot-relative paths of known arguments with ${pwd}.
+    flags = ["-fsanitize-ignorelist", "-isystem", "--sysroot"]
 
-    Args:
-        args (list): List of tool arguments.
+    def split_flag(flag):
+        if flag in flags:
+            return (flag, None)
+        for flag in flags:
+            s, opt, path = arg.partition(flag + "=")
+            if s == "":
+                return (opt, path)
+        return (None, None)
 
-    Returns:
-        list: The modified argument list.
-    """
-    res = []
-    fix_next_arg = False
     for arg in args:
         if fix_next_arg and not paths.is_absolute(arg):
             res.append("${{pwd}}/{}".format(arg))
+            fix_next_arg = False
         else:
-            res.append(arg)
-
-        fix_next_arg = arg == "-isystem"
+            opt, path = split_flag(arg)
+            if opt and path and not paths.is_absolute(path):
+                res.append("{}${{pwd}}/{}".format(opt, path))
+            else:
+                fix_next_arg = (opt and path == None)
+                res.append(arg)
 
     return res
 
-def _pwd_flags_fsanitize_ignorelist(args):
-    """Prefix execroot-relative paths of known arguments with ${pwd}.
-
-    Args:
-        args (list): List of tool arguments.
-
-    Returns:
-        list: The modified argument list.
-    """
-    res = []
-    for arg in args:
-        s, opt, path = arg.partition("-fsanitize-ignorelist=")
-        if s == "" and not paths.is_absolute(path):
-            res.append("{}${{pwd}}/{}".format(opt, path))
-        else:
-            res.append(arg)
-    return res
-
-def _pwd_flags(args):
-    return _pwd_flags_fsanitize_ignorelist(_pwd_flags_isystem(_pwd_flags_sysroot(args)))
-
 def _feature_enabled(ctx, feature_name, default = False):
     """Check if a feature is enabled.