Nanofiltration can be a useful tool to remove pharmaceuticals in water sources. The performance of the most used thin film composite (TFC) membranes, typically with a thin polyamide (PA) layer, can be improved using thin film nanocomposite (TFN) membranes obtained by the introduction of a filler within the PA layer. In this work, to control the positioning of the filler two kinds of PA/metal-organic framework (MOF) bilayered TFC (BTFC) membranes, PA/ZIF-93 and PA/HKUST-1, were synthesized onto polyimide supports. First, the interfacial synthesis was used for the preparation of a MOF layer, and second, a PA layer was synthesized by interfacial polymerization. These BTFC membranes were applied in the nanofiltration of diclofenac and naproxen aqueous solutions obtaining a maximum water permeance of 33.1 and 24.9 L.m(-2). h(-1)-bar(-1), respectively, with a rejection of >= 98% when HKUST-1 was used. These permeance improvements (using diclofenac, 4.9 and 3.4 times the value of the TFC and TFN membranes, respectively) are related to the PA layer thickness, MOF porosity, membrane hydrophilicity, and membrane roughness.