Abstract This study evaluated the effect of high pressure processing (HPP) on the proteolytic and milk-clotting activities of recombinant chymosin, bovine rennet and porcine pepsin. The optimum process conditions were established considering the maximum increase on milk-clotting activity, which was 10% for recombinant chymosin (212MPa/5min/10 °C) and the bovine rennet (222 MPa/5min/23 °C) and 6% for the porcine pepsin (50MPa/5min/20 °C). The high pressure (HP) processed enzymes promoted faster milk-clotting and the gels produced were more consistent (values of G' >6% and k' >5%). Processed enzymes produced gels with higher Δ backscattering measured using near-infrared (NIR) light (at least 6%), indicating higher degree of protein aggregation. Images obtained by confocal microscopy showed a faster reduction in the total number of pores, with an increased average pore area for gels obtained with the HP processed enzymes. Furthermore, the wet yields of the gels obtained from HP processed enzymes were up to 4.3% greater than gels obtained with non-processed enzymes. Thus, HPP emerges as an interesting alternative to improve the performance of milk-clotting enzymes, accelerating milk-clotting and allowing for an increase in cheese yield.