Nowadays polymer-based thin film nanocomposite (TFN) membrane technologies are showing key interest to improve the separation properties. TFN membranes are well known in diverse fields but developing highly improved TFN membranes for the removal of low concentration solutions is the main challenge for the researchers. Application of functional nanomaterials, incorporated in TFN membranes provides better performance as permeance and selectivity. The polymer membrane-based separation process plays an important role in the chemical industry for the isolation of products and recovery of different important types of reactants. Due to the reduction in investment, less operating costs and safety issues membrane methods are mainly used for the separation process. Membranes do good separation of dyes and ions, yet their separation efficiency is challenged when the impurity is in low concentration. Herewith, we have developed, UiO-66-NH2 incorporated TFN membranes through interfacial polymerization between piperazine (PIP) and trimesoyl chloride (TMC) for separating malachite green dye and phosphate from water in their low concentration. A comparative study between thin-film composite (TFC) and TFN has been carried out to comprehend the benefit of loading nanoparticles. To provide mechanical strength to the polyamide layer ultra-porous polysulfone support was made through phase inversion. As a result, outstanding separation values of malachite green (MG) 91.90 ± 3% rejection with 13.32 ± 0.6 Lm−2h−1 flux and phosphate 78.36 ± 3% rejection with 22.22 ± 1.1 Lm−2h−1 flux by TFN membrane were obtained. The antifouling tendency of the membranes was examined by using bovine serum albumin (BSA)-mixed feed and deionized water, the study showed a good ~84% antifouling tendency of TFN membrane with a small ~14% irreversible fouling. Membrane’s antibacterial test against E. coli. and S. aureus. also revealed that the TFN membrane possesses antibacterial activity as well. We believe that the present work is an approach to obtaining good results from the membranes under tricky conditions.