diff --git a/CMakeLists.txt b/CMakeLists.txt
index abfacf0358..27ce24a140 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -128,8 +128,6 @@ get_target_triple( NEST_TARGET_TRIPLE NEST_TARGET_ARCH NEST_TARGET_VENDOR NEST_T
 nest_process_with_python()
 include( GNUInstallDirs )
 nest_post_process_with_python()
-nest_process_with_optimize()
-nest_process_with_debug()
 nest_process_with_std()
 nest_process_with_intel_compiler_flags()
 nest_process_with_warning()
@@ -156,6 +154,12 @@ nest_process_version_suffix()
 nest_process_userdoc()
 nest_process_devdoc()
 
+# These two function calls must come last, as to prevent unwanted interactions of the newly set flags
+# with detection/compilation operations carried out in earlier functions. The optimize/debug flags set
+# using these functions should only apply to the compilation of NEST.
+nest_process_with_optimize()
+nest_process_with_debug()
+
 nest_get_color_flags()
 set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${NEST_C_COLOR_FLAGS}" )
 set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${NEST_CXX_COLOR_FLAGS}" )
diff --git a/cmake/ProcessOptions.cmake b/cmake/ProcessOptions.cmake
index da6a37fdfa..a540cfb4b0 100644
--- a/cmake/ProcessOptions.cmake
+++ b/cmake/ProcessOptions.cmake
@@ -22,13 +22,14 @@
 # add custom warnings and optimizations
 function( NEST_PROCESS_WITH_OPTIMIZE )
   if ( with-optimize )
-    if ( with-optimize STREQUAL "ON" )
+  string(TOUPPER "${with-optimize}" WITHOPTIMIZE)
+    if ( WITHOPTIMIZE STREQUAL "ON" )
       set( with-optimize "-O2" )
     endif ()
-    foreach ( flag ${with-optimize} )
-      set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${flag}" PARENT_SCOPE )
-      set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${flag}" PARENT_SCOPE )
-    endforeach ()
+    set(OPTIMIZATION_FLAGS "")
+    string(JOIN " " OPTIMIZATION_FLAGS  ${with-optimize} )
+    set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OPTIMIZATION_FLAGS}" PARENT_SCOPE )
+    set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OPTIMIZATION_FLAGS}" PARENT_SCOPE )
   endif ()
 endfunction()