The design of functional micro- and mesostructured composite materials is significantly important for separation processes. Mesoporous silica is an attractive material for fast diffusion, while microporous zeolitic imidazolate frameworks (ZIFs) are beneficial for selective adsorption and diffusion. In this work, ZIF-71 and ZIF-8 nanocrystals were grown on the surface of mesoporous silica spheres (MSS) via the seeding and regrowth approach in order to obtain monodispersed MSS–ZIF-71 and MSS–ZIF-8 spheres with a particle size of 2–3 μm. These MSS–ZIF spheres were uniformly dispersed into a polydimethylsiloxane (PDMS) matrix to prepare mixed matrix membranes (MMMs). These MMMs were evaluated for the separation of ethanol from water via pervaporation. The pervaporation results reveal that the MSS–ZIF filled MMMs substantially improve the ethanol recovery in both aspects viz. flux and separation factor. These MMMs outperforms the unfilled PDMS membranes and the conventional carbon and zeolite filled MMMs. As expected, the mesoporous silica core allows very fast flow of the permeating compound, while the hydrophobic ZIF coating enhances the ethanol selectivity through its specific pore structure, hydrophobicity and surface chemistry. It can be seen that ZIF-8 mainly has a positive impact on the selectivity, while ZIF-71 enhances fluxes more significantly.