diff --git a/simtbx/kokkos/SConscript b/simtbx/kokkos/SConscript
index 25d87173af..d1b3ca6a07 100644
--- a/simtbx/kokkos/SConscript
+++ b/simtbx/kokkos/SConscript
@@ -69,7 +69,10 @@ kokkos_cxxflags = subprocess.check_output(
   ['make', '-f', 'Makefile.kokkos', 'print-cxx-flags'],
   cwd=os.environ['KOKKOS_PATH'])
 kokkos_cxxflags = kokkos_cxxflags.split(b'\n')
-kokkos_cxxflags = kokkos_cxxflags[1].decode('utf8').split()
+# remove empty lines (this will also remove trailing \n in stdout)
+kokkos_cxxflags = list(filter(lambda x: x!=b'', kokkos_cxxflags))
+# last line returned by print-cxx-flags contains flags
+kokkos_cxxflags = kokkos_cxxflags[-1].decode('utf8').split()
 print('KOKKOS_CXXFLAGS:', kokkos_cxxflags)
 print('='*79)