diff --git a/.github/workflows/ports_unix.yml b/.github/workflows/ports_unix.yml
index 8fd8e1aec2..a1b91d5cf0 100644
--- a/.github/workflows/ports_unix.yml
+++ b/.github/workflows/ports_unix.yml
@@ -90,6 +90,7 @@ jobs:
       run: source tools/ci.sh && ci_unix_coverage_run_native_mpy_tests
     - name: Run gcov coverage analysis
       run: |
+        (cd mpy-cross && gcov -o build/py ../py/*.c || true)
         (cd ports/unix && gcov -o build-coverage/py ../../py/*.c || true)
         (cd ports/unix && gcov -o build-coverage/extmod ../../extmod/*.c || true)
     - name: Upload coverage to Codecov
diff --git a/tools/ci.sh b/tools/ci.sh
index 83b95b1f05..b00aac0bd5 100755
--- a/tools/ci.sh
+++ b/tools/ci.sh
@@ -637,6 +637,10 @@ function ci_unix_coverage_setup {
 }
 
 function ci_unix_coverage_build {
+    make ${MAKEOPTS} -C mpy-cross COPT="-Os -fprofile-arcs -ftest-coverage" LDFLAGS="-fprofile-arcs -ftest-coverage -lm" DEBUG=1
+    make ${MAKEOPTS} -C ports/unix VARIANT=coverage submodules
+    make ${MAKEOPTS} -C ports/unix VARIANT=coverage deplibs
+    make ${MAKEOPTS} -C ports/unix VARIANT=coverage
     ci_unix_build_helper VARIANT=coverage
     ci_unix_build_ffi_lib_helper gcc
 }