The majority of the silicon devices contain amorphous phase and amorphous/crystalline interfaces which both considerably affect the transport of energy carriers as phonons and electrons. In this article, we investigate the impact of amorphous phases (both amorphous silicon and amorphous SiO2) of silicon nanoporous membranes on their thermal properties via molecular dynamics simulations. We show that a small fraction of amorphous phase reduces dramatically the thermal transport. One can even create nanostructured materials with subamorphous thermal conductivity, while keeping an important crystalline fraction. In general, the a-SiO2 shell around the pores reduces the thermal conductivity by a factor of five to ten compared to a-Si shell. The phonon density of states for several systems is also given to give the impact of the amorphisation on the phonon modes.