The incorporation of nanomaterials in membrane’s matrix aims mainly to improve the properties of the membranes such as hydrophilicity, mechanical strength, thermal stability, water flux. Multi-walled carbon nanotubes (MWCNT) and functionalized graphene oxide (fGO) have recently attracted attention, as they have proved to have potential in various applications. In this study, self-assembled MWCNT-fGO nanocomposite was synthesized and used as a filler in environmentally-friendly polylactic acid (PLA) membranes. The membranes were fabricated following the phase inversion method with different concentrations of MWCNT-fGO (2, 4, 6 and 8 wt.%). In addition, the membranes were tested for the removal of heavy metal ions from wastewater. The results showed that a considerable removal can be achieved using the composite membranes. For instance, the highest Cu2+, Ni2+ and Zn2+ removal (e.g., 89%, 35%, and 39%, respectively) was observed in the 8 wt.% MWCNT-fGO PLA membrane. This was achieved at water flux of 850 L·m-2·h-1 (LMH). On the other hand, the pristine PLA membrane water flux was around 450 LMH and was capable of achieving 82, 25, and 30% rejections for Cu2+, Ni2+ and Zn2+, respectively. These results showed the potential of the MWCNT-fGO PLA membranes application in treating heavy-metal containing wastewater.