Polyamide (PA) membranes with a thin selective layer have been widely investigated for desalination and water treatment. Several modifications have been proposed over the years to tailor the morphology of such thin film composite (TFC) membranes by altering the support and/or selective layers to achieve superior performance. In this study, a facile approach towards fabricating a highly wrinkled selective layer has been demonstrated through bio-inspired modification of the support layer with Y-type zeolites. Results showed that incorporating zeolites in a smaller dimension (200 nm) produced by a unique ball milling technique is favorable for a defect-free selective layer in comparison to larger commercial zeolites. PA membranes formed by the interfacial polymerization (IP) of Piperazine (PIP) and 1,3,5-Benzenetricarbonyl trichloride (TMC) revealed highly wrinkled morphology due to the presence of zeolites in the TFC interlayer. At optimum fabrication conditions, the membrane exhibited a fast transport of 22.5 ± 2.2 Lm-2h-1bar-1 with a salt rejection of 48.6, 91.3, 99.1, and 99.5% for NaCl, MgCl2, MgSO4, and Na2SO4, respectively. Besides the unique preparation of zeolites in smaller dimensions, the novelty of this study lies in the facile membrane pretreatment before IP to achieve wrinkled PA membranes for enhanced nanofiltration performance.