diff --git a/examples/Makefile.am b/examples/Makefile.am
index a589b184350b9fddc7028d60709f18c2003a2bea..95057c9bee7d3b4cc001d6c19ca39cab5d8544c4 100644
--- a/examples/Makefile.am
+++ b/examples/Makefile.am
@@ -18,8 +18,8 @@
 # Common flags
 MYFLAGS = 
 
-# Add the source directory and debug to CFLAGS
-AM_CFLAGS = -I$(top_srcdir)/src $(HDF5_CPPFLAGS) $(GSL_INCS)
+# Add the source directory and the non-standard paths to the included library headers to CFLAGS
+AM_CFLAGS = -I$(top_srcdir)/src $(HDF5_CPPFLAGS) $(GSL_INCS) $(FFTW_INCS)
 
 AM_LDFLAGS = $(HDF5_LDFLAGS)
 
diff --git a/src/Makefile.am b/src/Makefile.am
index e21cb6539d2b7ae360ea07c92c426e99342bc2ec..d8b633fe1e97e67fc4ef0cc29bab8f6fd25fd907 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -15,8 +15,8 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-# Add the debug flag to the whole thing
-AM_CFLAGS = $(HDF5_CPPFLAGS) $(GSL_INCS)
+# Add the non-standard paths to the included library headers
+AM_CFLAGS = $(HDF5_CPPFLAGS) $(GSL_INCS) $(FFTW_INCS)
 
 # Assign a "safe" version number
 AM_LDFLAGS = $(HDF5_LDFLAGS) $(FFTW_LIBS) -version-info 0:0:0
diff --git a/tests/Makefile.am b/tests/Makefile.am
index 8a757e0b87ffae4d6daa1a6f2b67cf9548b868d0..643d89aaf05e31b6ea1c304c4fac6c28f7e89d03 100644
--- a/tests/Makefile.am
+++ b/tests/Makefile.am
@@ -14,8 +14,8 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-# Add the source directory and debug to CFLAGS
-AM_CFLAGS = -I$(top_srcdir)/src $(HDF5_CPPFLAGS) $(GSL_INCS)
+# Add the source directory and the non-standard paths to the included library headers to CFLAGS
+AM_CFLAGS = -I$(top_srcdir)/src $(HDF5_CPPFLAGS) $(GSL_INCS) $(FFTW_INCS)
 
 AM_LDFLAGS = ../src/.libs/libswiftsim.a $(HDF5_LDFLAGS) $(HDF5_LIBS) $(FFTW_LIBS) $(GRACKLE_LIBS) $(GSL_LIBS)