diff --git a/.gitignore b/.gitignore
index 54b3c5496..7224e92f8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,6 +2,9 @@
 seedfile
 # MBEDTLS_PSA_INJECT_ENTROPY seed file created by the test framework
 00000000ffffff52.psa_its
+# Log files created by all.sh to reduce the logs in case a component runs
+# successfully
+quiet-make.*
 
 # CMake build artifacts:
 CMakeCache.txt
diff --git a/pkgconfig/.gitignore b/pkgconfig/.gitignore
new file mode 100644
index 000000000..5460c2076
--- /dev/null
+++ b/pkgconfig/.gitignore
@@ -0,0 +1,2 @@
+Makefile
+*.pc
diff --git a/tests/scripts/all.sh b/tests/scripts/all.sh
index 1e57ac7c1..d46ec2291 100755
--- a/tests/scripts/all.sh
+++ b/tests/scripts/all.sh
@@ -304,8 +304,9 @@ cleanup()
            \( -iname cmake_install.cmake -o \
               -iname CTestTestfile.cmake -o \
               -iname CMakeCache.txt \) -exec rm {} \+
-    # Recover files overwritten by in-tree CMake builds
-    rm -f include/Makefile include/mbedtls/Makefile programs/!(fuzz)/Makefile
+    # Remove Makefiles generated by in-tree CMake builds
+    rm -f 3rdparty/Makefile 3rdparty/*/Makefile pkgconfig/Makefile
+    rm -f include/Makefile programs/!(fuzz)/Makefile
 
     # Remove any artifacts from the component_test_cmake_as_subdirectory test.
     rm -rf programs/test/cmake_subproject/build