The formation of emulsions with micro-engineered silicon based arrays of micro-orifices is a relatively new technique. Until now, only the preparation of oil-in-water emulsions was studied due to the hydrophilic nature of silicon. This work evaluates the emulsification of water into n-hexadecane with hydrophobized arrays of micro-orifices. We have studied the drop formation rate, the number of active pores and the drop size. In contrast to conventional macroporous membranes used for membrane emulsification, we observed high dispersed phase fluxes up to 4600 L h−1 m−2 bar−1 while all pores being active at applied pressures below 2 times the critical pressure. The drop diameter was independent from the applied pressure difference. We observed a pressure dependent lag time between drop formations at low emulsification pressures. The lag time is related to the rate of surfactant diffusion to the water–oil interface causing a reduction of the interfacial tension. A significant influence of the used hydrophobization agents, perfluorinated octyltrichlorosilane (FOTS) and octyltrichlorosilane (OTS), was found for the resulting drop sizes and the number of active pores.