Membrane-based technologies used for water treatment can be an excellent alternative to handle wastewater including both conventional and emerging pollutants as they can provide technological (e.g., high quality of treated water) and economic (e.g., small footprint and low unit cost of production) advantages over other water treatment processes. Recently, low cost ceramic membranes fabricated from natural resources like kaolinitic clay, bentonite clay, phosphate are increasingly used owing to their low-cost starting materials, low sintering temperature and their excellent additional properties. Moreover, the modification of the surface by grafting process provides membranes appropriate for low UF process (dp < 10 nm) and suitable for micropollutants removal at relatively high permeate flux value which can be maintained during filtration due to antifouling characteristics of the UF active layer. In this work, the surface of microfiltration membranes made from natural zeolite was chemically modified by grafting with 1 H, 1 H, 2 H, 2 H-perfluorodecyltriethoxysilane molecule named PFAS. Various characterization methods and techniques, including scanning electron microscopy (SEM), mercury porosimetry, FTIR, TGA, and contact angle, were used to check the properties of the membranes surface before and after grafting. The grafted membranes pore size and porosity were reduced, as proved by SEM images. The determination of the water permeability shows a reduction from 1218 L.h−1.m−2.bar −1 to 204 L.h−1.m−2.bar −1 which confirm the surface densification. The application of the grafted membrane to the treatment of Indigo Blue (IB) colored solution and oily wastewater was investigated to evaluate the performances of this membrane in terms of permeate flux and pollutants retention. The filtration results revealed a good retention of color and oil, exceeding 95% for both parameters. Therefore, it is interesting to recommend this new low-cost membrane for the treatment of industrial wastewater containing recalcitrant pollutants such as color. The study of the effect of the treated colored solution on plant growth, shows that the presence of some residual nutrients required for crops growth, might make the IB treated water beneficial for irrigation purposes.