diff --git a/Makefile b/Makefile
index 124c37fdb0..62fd43ffab 100644
--- a/Makefile
+++ b/Makefile
@@ -200,8 +200,12 @@ check_format:
 
 check: px4fmu-v1_default px4fmu-v2_default px4fmu-v4_default px4-stm32f4discovery_default check_format tests
 
-tests: posix_sitl_default
-	@(cd unittests && ./run_tests.sh)
+unittest: posix_sitl_default
+	@(cd unittests && cmake -G$(PX4_CMAKE_GENERATOR) && $(PX4_MAKE) $(PX4_MAKE_ARGS) && ctest)
+
+tests: unittest
+	@make --no-print-directory px4fmu-v2_default test
+	@make --no-print-directory posix_sitl_default test
 
 package_firmware:
 	@zip --junk-paths Firmware.zip `find . -name \*.px4`
diff --git a/unittests/.gitignore b/unittests/.gitignore
index e9d1bc3e01..4f34a742f7 100644
--- a/unittests/.gitignore
+++ b/unittests/.gitignore
@@ -15,3 +15,8 @@ CMakeFiles
 CTestTestfile.cmake
 cmake_install.cmake
 Makefile
+.ninja_deps
+.ninja_log
+build.ninja
+rules.ninja
+
diff --git a/unittests/run_tests.sh b/unittests/run_tests.sh
deleted file mode 100755
index 979f8c95dd..0000000000
--- a/unittests/run_tests.sh
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/bin/sh
-
-cmake .
-make --no-print-directory clean
-make --no-print-directory all -j4
-
-set -e
-
-#./param_test
-./conversion_test
-./autodeclination_test
-./mixer_test 2> /dev/null
-./sbus2_test
-./rc_input_test