diff --git a/python/Makefile b/python/Makefile
index 9649addc6d2d780321efbf2a9f744813032b6aea..862e97c4a0ab14d918b6ebd34ff9226cd4dc7193 100644
--- a/python/Makefile
+++ b/python/Makefile
@@ -15,6 +15,7 @@ all:
 	@echo Building python interface for PLUMED 
 	unset CXX && unset CC && unset CFLAGS && unset CXXFLAGS && unset LDSHARED && \
           plumed_program_name=plumed \
+          plumed_force_cython=yes \
           plumed_version=$(VERSION) \
           plumed_include_dir=../src/wrapper \
           plumed_default_kernel="$$PWD/../src/lib/libplumedKernel.$(SOEXT)" \
diff --git a/src/lib/Makefile b/src/lib/Makefile
index e6df6c5c96e5ca6062ede14989669091449eab4c..cc6860104ea67ce73a506aab8f3fe3602aa5862f 100644
--- a/src/lib/Makefile
+++ b/src/lib/Makefile
@@ -314,6 +314,7 @@ ifdef python_bin
 	cd install/python && rm -fr *.so plumed.cpp build && \
           unset CXX && unset CC && unset CFLAGS && unset CXXFLAGS && unset LDSHARED && \
           plumed_program_name=plumed \
+          plumed_force_cython=yes \
           plumed_version=$(VERSION) \
           plumed_include_dir=../../../wrapper \
           plumed_default_kernel="$(libdir)/lib$(program_name)Kernel.$(SOEXT)" \