Hydrophilic ultrafiltration membranes made of polyamide with molecular weight cutoff 10 and 50 kDa have been studied for the preparation of oil-in-water emulsions by a cross-flow membrane emulsification technique. Isooctane and phosphate buffer were used as disperse and continuous phase, respectively. The permeation of apolar isooctane through the polar hydrophilic membrane was achieved by pretreatment of membranes with a gradient of miscible solvents of decreasing polarity to remove water from the pores and replace it with isooctane. Four different procedures were investigated, based on the solvent mixture percentage and contact time with membranes. After pretreatment, the performance of the membranes in terms of pure isooctane permeate flux and emulsion preparation was evaluated. The influence of organic solvents on polyamide (PA) membranes has been studied by SEM analysis, which showed a clear change in the structure and morphology of the thin selective layers. The effects proved stronger for PA 10 kDa than for 50 kDa. In fact, similar pretreatment procedures caused larger pore size and pore size distribution for PA 10 kDa than for 50 kDa. The properties of emulsions in terms of droplet size distribution reflected the membrane pore sizes obtained after pretreatment. The correlation between pore size and droplet size, for the physicochemical and fluid dynamic conditions used, has been evaluated.