diff --git a/cscs-checks/compile/src/haswell_fma/Makefile b/cscs-checks/compile/src/haswell_fma/Makefile
index bddaf178c6..c836e42f2b 100644
--- a/cscs-checks/compile/src/haswell_fma/Makefile
+++ b/cscs-checks/compile/src/haswell_fma/Makefile
@@ -7,7 +7,7 @@ vectorize_fma_cplusplus: vectorize_fma_cplusplus.cc
 	$(CXX) $(CXXFLAGS) vectorize_fma_cplusplus.cc
 
 vectorize_fma_ftn: vectorize_fma_ftn.f90
-	$(FC) $(FFLAGS) vectorize_fma_ftn.f90
+	$(FC) $(FCFLAGS) vectorize_fma_ftn.f90
 
 clean:
 	rm *.s
diff --git a/cscs-checks/tools/profiling_and_debugging/src/F90/Makefile b/cscs-checks/tools/profiling_and_debugging/src/F90/Makefile
index 7cadf76e7c..fa0744e2e9 100644
--- a/cscs-checks/tools/profiling_and_debugging/src/F90/Makefile
+++ b/cscs-checks/tools/profiling_and_debugging/src/F90/Makefile
@@ -6,10 +6,10 @@ all: jacobi
 OBJS :=  _variableDef.o _jacobi.o _main.o
 
 $(OBJS):
-	$(PREP) $(FC) $(FFLAGS) -c -o $(@) $(@:.o=.F90)
+	$(PREP) $(FC) $(FCFLAGS) -c -o $(@) $(@:.o=.F90)
 
 $(EXECUTABLE): $(OBJS)
-	$(PREP) $(FC) $(FFLAGS) $(LDFLAGS) -o $(@) $(OBJS)
+	$(PREP) $(FC) $(FCFLAGS) $(LDFLAGS) -o $(@) $(OBJS)
 
 clean:
 	-$(RM) $(OBJS) *.mod
diff --git a/cscs-checks/tools/profiling_and_debugging/src/F90/Makefile_perftools b/cscs-checks/tools/profiling_and_debugging/src/F90/Makefile_perftools
index 55439382a1..a7ad6624a3 100644
--- a/cscs-checks/tools/profiling_and_debugging/src/F90/Makefile_perftools
+++ b/cscs-checks/tools/profiling_and_debugging/src/F90/Makefile_perftools
@@ -7,7 +7,7 @@ LIB            =
 .SUFFIXES: .o .F90
 
 %.o: %.F90
-	$(FC) $(CPPFLAGS) $(FFLAGS) -c $< -o $(PE_ENV)$@
+	$(FC) $(CPPFLAGS) $(FCFLAGS) -c $< -o $(PE_ENV)$@
 
 perftools_check: $(OBJ)
 	$(LD) $(LDFLAGS) $(OBJ2) $(LIB) -o $@
diff --git a/cscs-checks/tools/profiling_and_debugging/src/F90/Makefile_scorep_mpi_omp b/cscs-checks/tools/profiling_and_debugging/src/F90/Makefile_scorep_mpi_omp
index 990c4a43b1..1d6d834201 100644
--- a/cscs-checks/tools/profiling_and_debugging/src/F90/Makefile_scorep_mpi_omp
+++ b/cscs-checks/tools/profiling_and_debugging/src/F90/Makefile_scorep_mpi_omp
@@ -7,12 +7,12 @@ OBJS :=  _variableDef.o _jacobi.o _main.o
 
 $(OBJS):
 	@echo 'Compiling: $@'
-	@echo '$(PREP) $(FC) $(FFLAGS) -c -o $(@) $(@:.o=.F90)'
-	$(PREP) $(FC) $(FFLAGS) -c -o $(@) $(@:.o=.F90)
+	@echo '$(PREP) $(FC) $(FCFLAGS) -c -o $(@) $(@:.o=.F90)'
+	$(PREP) $(FC) $(FCFLAGS) -c -o $(@) $(@:.o=.F90)
 
 $(EXECUTABLE): $(OBJS)
 	@echo 'Linking: $@'
-	$(PREP) $(FC) $(FFLAGS) $(LDFLAGS) -o $(@) $(OBJS)
+	$(PREP) $(FC) $(FCFLAGS) $(LDFLAGS) -o $(@) $(OBJS)
 	@echo 'Finished building: $@'
 	@echo ' '