diff --git a/cargo/private/cargo_build_script.bzl b/cargo/private/cargo_build_script.bzl
index b1c630a86e..cac1c60fb7 100644
--- a/cargo/private/cargo_build_script.bzl
+++ b/cargo/private/cargo_build_script.bzl
@@ -110,12 +110,18 @@ def _should_prefix_pwd(path):
     if paths.is_absolute(path):
         return False
 
+    if path.startswith("${pwd}"):
+        return False
+
     for placeholder in _BAZEL_PATH_PLACEHOLDERS:
         if path.startswith(placeholder):
             return False
 
     return True
 
+def _expects_space_separated_arg(flag):
+    return not (flag.endswith("=") or flag.endswith(":"))
+
 def _prefix_pwd_to_flag(args, flag_variations):
     """Prefix execroot-relative paths for flags that support both concatenated and space-separated forms (unless it ends with `=` or `:`).
 
@@ -144,18 +150,16 @@ def _prefix_pwd_to_flag(args, flag_variations):
         handled = False
         new_prefix_next_arg = False
 
-        for flag in flag_variations:
+        for flag in sorted(flag_variations, key = len, reverse = True):
             # Check for exact match first
             if arg == flag:
-                if flag.endswith("=") or flag.endswith(":"):
-                    # Flag ending with '=' or ':' and empty path: keep as-is
-                    res.append(arg)
-                    handled = True
-                    break
-                else:
+                if _expects_space_separated_arg(flag):
                     # Flag without '=' or ':': next arg might be space-separated path
                     new_prefix_next_arg = True
-                continue
+
+                res.append(arg)
+                handled = True
+                break
 
             # Check for concatenated form (flag with path)
             if arg.startswith(flag):
@@ -168,8 +172,10 @@ def _prefix_pwd_to_flag(args, flag_variations):
                 handled = True
                 break
 
-            # Check for space-separated form (only for flags without '=' or ':')
-            if not flag.endswith("=") and not flag.endswith(":") and prefix_next_arg and _should_prefix_pwd(arg.strip()):
+            # Check for space-separated form (only for flags without '=' or ':').
+            # A leading '-' means the flag's value was omitted and this is
+            # actually the next flag, not a path; leave it untouched.
+            if _expects_space_separated_arg(flag) and prefix_next_arg and not arg.strip().startswith("-") and _should_prefix_pwd(arg.strip()):
                 res.append("${{pwd}}/{}".format(arg.strip()))
                 handled = True
                 break
@@ -260,8 +266,21 @@ def _pwd_paths(args):
     """Prefix execroot-relative paths with ${pwd}."""
     return _prefix_pwd_to_paths(args)
 
+_PWD_FLAG_PASSES = [
+    _pwd_flags_sysroot,
+    _pwd_flags_resource_dir,
+    _pwd_flags_B,
+    _pwd_flags_L,
+    _pwd_flags_isystem,
+    _pwd_flags_fsanitize_ignorelist,
+    _pwd_flags_imacros,
+    _pwd_flags_direct_libs,
+]
+
 def _pwd_flags(args):
-    return _pwd_flags_direct_libs(_pwd_flags_imacros(_pwd_flags_fsanitize_ignorelist(_pwd_flags_isystem(_pwd_flags_L(_pwd_flags_B(_pwd_flags_resource_dir(_pwd_flags_sysroot(args))))))))
+    for pwd_flags_pass in _PWD_FLAG_PASSES:
+        args = pwd_flags_pass(args)
+    return args
 
 def _feature_enabled(ctx, feature_name, default = False):
     """Check if a feature is enabled.
diff --git a/cargo/tests/cargo_build_script/cc_args_and_env/BUILD.bazel b/cargo/tests/cargo_build_script/cc_args_and_env/BUILD.bazel
index 496dfb5a2b..a2c9cd7c98 100644
--- a/cargo/tests/cargo_build_script/cc_args_and_env/BUILD.bazel
+++ b/cargo/tests/cargo_build_script/cc_args_and_env/BUILD.bazel
@@ -1,8 +1,10 @@
 load(
     "cc_args_and_env_test.bzl",
     "bindir_absolute_test",
+    "bindir_malformed_missing_value_test",
     "bindir_relative_test",
     "direct_libs_absolute_test",
+    "direct_libs_as_flag_operand_test",
     "direct_libs_relative_test",
     "fsanitize_ignorelist_absolute_test",
     "fsanitize_ignorelist_relative_test",
@@ -12,10 +14,12 @@ load(
     "include_mixed_test",
     "include_relative_test",
     "isystem_absolute_test",
+    "isystem_after_relative_test",
     "isystem_relative_test",
     "legacy_cc_toolchain_test",
     "libpath_absolute_test",
     "libpath_relative_test",
+    "libpath_separated_relative_test",
     "resource_dir_absolute_test",
     "resource_dir_relative_test",
     "sysroot_absolute_test",
@@ -38,6 +42,8 @@ isystem_relative_test(name = "isystem_relative_test")
 
 isystem_absolute_test(name = "isystem_absolute_test")
 
+isystem_after_relative_test(name = "isystem_after_relative_test")
+
 xclang_isystem_relative_test(name = "xclang_isystem_relative_test")
 
 xclang_isystem_absolute_test(name = "xclang_isystem_absolute_test")
@@ -46,6 +52,8 @@ bindir_relative_test(name = "bindir_relative_test")
 
 bindir_absolute_test(name = "bindir_absolute_test")
 
+bindir_malformed_missing_value_test(name = "bindir_malformed_missing_value_test")
+
 fsanitize_ignorelist_absolute_test(name = "fsanitize_ignorelist_absolute_test")
 
 fsanitize_ignorelist_relative_test(name = "fsanitize_ignorelist_relative_test")
@@ -60,6 +68,8 @@ libpath_absolute_test(name = "libpath_absolute_test")
 
 libpath_relative_test(name = "libpath_relative_test")
 
+libpath_separated_relative_test(name = "libpath_separated_relative_test")
+
 resource_dir_absolute_test(name = "resource_dir_absolute_test")
 
 resource_dir_relative_test(name = "resource_dir_relative_test")
@@ -73,3 +83,5 @@ include_mixed_test(name = "include_mixed_test")
 direct_libs_relative_test(name = "direct_libs_relative_test")
 
 direct_libs_absolute_test(name = "direct_libs_absolute_test")
+
+direct_libs_as_flag_operand_test(name = "direct_libs_as_flag_operand_test")
diff --git a/cargo/tests/cargo_build_script/cc_args_and_env/cc_args_and_env_test.bzl b/cargo/tests/cargo_build_script/cc_args_and_env/cc_args_and_env_test.bzl
index 6bd74edd06..663650e46b 100644
--- a/cargo/tests/cargo_build_script/cc_args_and_env/cc_args_and_env_test.bzl
+++ b/cargo/tests/cargo_build_script/cc_args_and_env/cc_args_and_env_test.bzl
@@ -463,6 +463,18 @@ def isystem_absolute_test(name):
         expected_cflags = ["-isystem", "/test/absolute/path"],
     )
 
+def isystem_after_relative_test(name):
+    """Regression test: a longer flag spelling must win over a shorter prefix."""
+    cargo_build_script_with_extra_cc_compile_flags(
+        name = "%s/cargo_build_script" % name,
+        extra_cc_compile_flags = ["-isystem-after", "test/relative/path"],
+    )
+    cc_args_and_env_analysis_test(
+        name = name,
+        target_under_test = "%s/cargo_build_script" % name,
+        expected_cflags = ["-isystem-after", "${pwd}/test/relative/path"],
+    )
+
 def bindir_relative_test(name):
     cargo_build_script_with_extra_cc_compile_flags(
         name = "%s/cargo_build_script" % name,
@@ -485,6 +497,18 @@ def bindir_absolute_test(name):
         expected_cflags = ["-B", "/test/absolute/path"],
     )
 
+def bindir_malformed_missing_value_test(name):
+    """Regression test: `-B` with no path must not swallow the next, unrelated flag."""
+    cargo_build_script_with_extra_cc_compile_flags(
+        name = "%s/cargo_build_script" % name,
+        extra_cc_compile_flags = ["-B", "-Wall"],
+    )
+    cc_args_and_env_analysis_test(
+        name = name,
+        target_under_test = "%s/cargo_build_script" % name,
+        expected_cflags = ["-B", "-Wall"],
+    )
+
 def fsanitize_ignorelist_relative_test(name):
     cargo_build_script_with_extra_cc_compile_flags(
         name = "%s/cargo_build_script" % name,
@@ -540,6 +564,18 @@ def libpath_absolute_test(name):
         expected_cflags = ["-L/test/absolute/sysroot", "-L", "/test/absolute/sysroot2", "-LIBPATH:/test/absolute/sysroot3", "-LIBPATH=/test/absolute/sysroot4", "-LIBPATH:", "some_unrelated_arg", "-LIBPATH=", "some_unrelated_arg2"],
     )
 
+def libpath_separated_relative_test(name):
+    """Regression test: bare `-LIBPATH` must not be matched as `-L` + `IBPATH`."""
+    cargo_build_script_with_extra_cc_compile_flags(
+        name = "%s/cargo_build_script" % name,
+        extra_cc_compile_flags = ["-LIBPATH", "test/relative/sysroot", "-LIBPATH", "/test/absolute/sysroot"],
+    )
+    cc_args_and_env_analysis_test(
+        name = name,
+        target_under_test = "%s/cargo_build_script" % name,
+        expected_cflags = ["-LIBPATH", "${pwd}/test/relative/sysroot", "-LIBPATH", "/test/absolute/sysroot"],
+    )
+
 def resource_dir_relative_test(name):
     cargo_build_script_with_extra_cc_compile_flags(
         name = "%s/cargo_build_script" % name,
@@ -656,3 +692,15 @@ def direct_libs_absolute_test(name):
         target_under_test = "%s/cargo_build_script" % name,
         expected_cflags = ["/test/absolute/libclang_rt.builtins.static.a", "/test/absolute/obj.o", "/test/absolute/libfoo.so", "/test/absolute/libbar.dylib", "some_unrelated_arg"],
     )
+
+def direct_libs_as_flag_operand_test(name):
+    """Regression test: an operand already rewritten must not be rewritten twice."""
+    cargo_build_script_with_extra_cc_compile_flags(
+        name = "%s/cargo_build_script" % name,
+        extra_cc_compile_flags = ["-imacros", "test/relative/libfoo.a", "-B", "test/relative/obj.o"],
+    )
+    cc_args_and_env_analysis_test(
+        name = name,
+        target_under_test = "%s/cargo_build_script" % name,
+        expected_cflags = ["-imacros", "${pwd}/test/relative/libfoo.a", "-B", "${pwd}/test/relative/obj.o"],
+    )