diff --git a/Makefile.am b/Makefile.am
index 3f81463..8ae0413 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -160,6 +160,7 @@ $(HTML_FILES): docs/index.html
 SWIG          = @SWIG@ 
 HDF5_LDFLAGS  = @HDF5_LDFLAGS@ 
 HDF5_CFLAGS   = @HDF5_CFLAGS@ 
+HDF5_CPPFLAGS = @HDF5_CPPFLAGS@ 
 
 if TREXIO_DEVEL
 
@@ -203,7 +204,7 @@ python-test: $(TEST_PY)
 
 python-install: $(pytrexio_py) $(setup_py) $(setup_cfg)
 	cd python && \
-		./install_pytrexio.sh $(HDF5_CFLAGS) $(HDF5_LDFLAGS)
+		./install_pytrexio.sh $(HDF5_CFLAGS) $(HDF5_CPPFLAGS) $(HDF5_LDFLAGS)
 
 python-sdist: $(pytrexio_py) $(setup_py) $(setup_cfg)
 	cd python && \
diff --git a/python/install_pytrexio.sh b/python/install_pytrexio.sh
index 81cde9f..bdcad50 100755
--- a/python/install_pytrexio.sh
+++ b/python/install_pytrexio.sh
@@ -3,17 +3,40 @@
 set -x
 set -e
 
-H5_CFLAGS_LOCAL=$1
-H5_LDFLAGS_LOCAL=$2
+# the parser below is needed when ./configure outputs several HDF5-related flags, which are then provided as input arguments to this script
+for arg in "$@"
+do
+    if [[ $arg == "-L"* ]] && [[ $arg == *"hdf5"* ]]; then
+        H5_LDFLAGS_LOCAL=$arg
+    elif [[ $arg == "-I"* ]] && [[ $arg == *"hdf5"* ]]; then
+        H5_CFLAGS_LOCAL=$arg
+    fi
+done
 
+# check that both variables are set
+if [[ -z ${H5_LDFLAGS_LOCAL} ]] || [[ -z ${H5_CFLAGS_LOCAL} ]]; then
+    echo "Paths to the HDF5 installation are not found. pkgconfig Python package will try to detect them."
+else
+    # additional explicit export was needed on MacOS
+    export H5_LDFLAGS=${H5_LDFLAGS_LOCAL}
+    export H5_CFLAGS=${H5_CFLAGS_LOCAL}
+fi
 
 # Install/upgrade packages required for the installation
 python3 -m pip install --upgrade setuptools wheel twine
 python3 -m pip install -r requirements.txt
 
+# export NUMPY_INCLUDEDIR environment variable needed for the proper setup
+source tools/set_NUMPY_INCLUDEDIR.sh
+
+if [[ -z ${NUMPY_INCLUDEDIR} ]] ; then
+    echo "NUMPY_INCLUDEDIR is not set. Check that numpy is installed (e.g. call pip freeze)."
+    exit 1
+fi
+
 # Create build directory and compile extension files (*.c)
 # --no-user-cfg disables custom .cfg files of the user machine, so that only setup.cfg is used
-H5_LDFLAGS=${H5_LDFLAGS_LOCAL} H5_CFLAGS=${H5_CFLAGS_LOCAL} python3 -s setup.py --no-user-cfg build 
+python3 -s setup.py --no-user-cfg build 
 
 # Local inplace build of the .so module with SWIG-produced pytrexio_wrap.c (from the SWIG documentation)
 #python3 setup.py build_ext --inplace --swig-opts="-modern"