diff --git a/pyodide_build/buildpkg.py b/pyodide_build/buildpkg.py
index 22d227b..6ad323b 100755
--- a/pyodide_build/buildpkg.py
+++ b/pyodide_build/buildpkg.py
@@ -549,7 +549,11 @@ def _get_helper_vars(self) -> dict[str, str]:
             "DISTDIR": str(self.src_dist_dir),
             # TODO: rename this to something more compatible with Makefile or CMake conventions
             "WASM_LIBRARY_DIR": str(self.library_install_prefix),
-            # Using PKG_CONFIG_LIBDIR instead of PKG_CONFIG_PATH,
+            # Emscripten will use this variable to configure pkg-config in emconfigure
+            "EM_PKG_CONFIG_PATH": str(self.library_install_prefix / "lib/pkgconfig"),
+            # This variable is usually overwritten by emconfigure
+            # The value below will only be used if pkg-config is called without emconfigure
+            # We use PKG_CONFIG_LIBDIR instead of PKG_CONFIG_PATH,
             # so pkg-config will not look in the default system directories
             "PKG_CONFIG_LIBDIR": str(self.library_install_prefix / "lib/pkgconfig"),
         }
diff --git a/pyodide_build/tests/test_buildpkg.py b/pyodide_build/tests/test_buildpkg.py
index c320c20..33b8a8f 100644
--- a/pyodide_build/tests/test_buildpkg.py
+++ b/pyodide_build/tests/test_buildpkg.py
@@ -126,6 +126,9 @@ def test_get_helper_vars(tmp_path):
         tmp_path / "pkg_1" / "build" / "pkg_1-1.0.0" / "dist"
     )
     assert helper_vars["WASM_LIBRARY_DIR"] == str(tmp_path / ".libs")
+    assert helper_vars["EM_PKG_CONFIG_PATH"] == str(
+        tmp_path / ".libs" / "lib" / "pkgconfig"
+    )
     assert helper_vars["PKG_CONFIG_LIBDIR"] == str(
         tmp_path / ".libs" / "lib" / "pkgconfig"
     )