Solvents purification mainly used in pharmaceutical field such as acetone and methyl ethyl ketone (MEK) were performed through hybrid silica membranes and from binary and multi-components mixtures. Two hybrid silica membranes—zirconia doped bis(triethoxysilyl)methane and bis(triethoxysilyl)ethane (BTESE)—were studied. Flux, permeance, and separation factor were evaluated depending on temperature, composition, and number of organic compounds in the feed. Dehydration tests of acetone were operated at 30 and 45 °C following by acetone and MEK purification at 50 °C from multi-components hydro-organic mixtures where hydrophilic compounds (water, methanol) but also hydrophobic (dichloromethane (DCM) and/or toluene) were present. Results showed that the presence of Zr nanoparticles affected flux and improved selectivity in the case of dehydration. Experiments related to acetone and MEK purification, revealed a mass transfer alteration and a decrease of performance, from 99 to 97 wt% and from 98 to 95 wt% respectively, when the number of compounds in the initial feed grown up and more precisely, in the presence of DCM and toluene thus highlighting a possible coupling effect.