diff --git a/bazel/config/generate_config_header.bzl b/bazel/config/generate_config_header.bzl
index 188655d93a5..6cc865bcbe4 100644
--- a/bazel/config/generate_config_header.bzl
+++ b/bazel/config/generate_config_header.bzl
@@ -24,6 +24,18 @@ def generate_config_header_impl(ctx):
         action_name = ACTION_NAMES.cpp_compile,
         variables = compile_variables,
     )
+
+    # The config header generation should not fail due to compiler warnings,
+    # so remove any flags that would treat warnings as errors.
+    compiler_flags = [
+        flag
+        for flag in compiler_flags
+        if not (
+            flag == "-Werror" or
+            flag.startswith("-Werror") or
+            flag == "/WX"
+        )
+    ]
     link_flags = cc_common.get_memory_inefficient_command_line(
         feature_configuration = feature_configuration,
         action_name = ACTION_NAMES.cpp_link_executable,
diff --git a/bazel/toolchains/cc/mongo_custom_features.bzl b/bazel/toolchains/cc/mongo_custom_features.bzl
index 31c64f9c6b7..6589b47c0ae 100644
--- a/bazel/toolchains/cc/mongo_custom_features.bzl
+++ b/bazel/toolchains/cc/mongo_custom_features.bzl
@@ -425,7 +425,7 @@ def get_common_features(ctx):
         ),
         feature(
             name = "warnings_as_errors_compile",
-            enabled = False,
+            enabled = ctx.attr.warnings_as_errors_enabled,
             flag_sets = [
                 flag_set(
                     actions = all_compile_actions,