diff --git a/docs/project/changelog.md b/docs/project/changelog.md
index 22ff1eff0..21d1b0441 100644
--- a/docs/project/changelog.md
+++ b/docs/project/changelog.md
@@ -151,6 +151,9 @@ substitutions:
   key was used for this purpose.
   {pr}`3006`
 
+- {{ Fix }} Fixed a bug that `backend-flags` propagated to dependencies.
+  {pr}`3153`
+
 ## Version 0.21.3
 
 _September 15, 2022_
diff --git a/pyodide-build/pyodide_build/pypabuild.py b/pyodide-build/pyodide_build/pypabuild.py
index 2eb92e955..a48adb89e 100644
--- a/pyodide-build/pyodide_build/pypabuild.py
+++ b/pyodide-build/pyodide_build/pypabuild.py
@@ -98,16 +98,9 @@ def _build_in_isolated_env(
         symlink_unisolated_packages(env)
         install_reqs(env, builder.build_system_requires)
         installed_requires_for_build = False
-        # "--build-option" contains custom options that only apply to current package,
-        # passing it to the dependencies may cause error.
-        # e.g., lightgbm accepts "--nomp" as one of its setup.py arguments,
-        # but "--nomp" isn't supported by its dependencies such as numpy, scipy, etc.
-        reqs_config_settings = {
-            k: v for k, v in config_settings.items() if k != "--build-option"
-        }
         try:
             build_reqs = builder.get_requires_for_build(
-                distribution, reqs_config_settings
+                distribution,
             )
         except BuildBackendException:
             pass
@@ -119,7 +112,9 @@ def _build_in_isolated_env(
             if not installed_requires_for_build:
                 install_reqs(
                     env,
-                    builder.get_requires_for_build(distribution, reqs_config_settings),
+                    builder.get_requires_for_build(
+                        distribution,
+                    ),
                 )
             return builder.build(distribution, outdir, config_settings)