Milk-clotting enzymes used in the dairy industry can be obtained from different sources such as plants, animals, and microorganisms. Recombinant chymosin is the best alternative for the dairy industry due to the differences in physicochemical properties of coagulating enzymes and scarcity of chymosin from animal sources. In this study, glycosylated and non-glycosylated forms of yak chymosin were extracellularly produced in a methylotrophic yeast, Komagataella phaffii (Pichia pastoris). Synthetic yak prochymosin genes were cloned into the pPICZ alpha A vector, expressed in P. pastoris GS115 (PDI) strain. Active chymosin expression was achieved into supernatant with Saccharomyces cerevisiae alpha-mating factor under the control of methanol-inducible AOXI promoter. The glycosylation of yak chymosin did not have a significant effect on yield and activity at shake flask level. In a 5L fermentor, production of native yak-chymosin was achieved and the enzyme activity was found as 214 IMCU/ml. pH of 6-7 and temperature of 40 degrees C values were optimum for the enzyme. The laboratory scale white cheese production yield with recombinant yak chymosin was very similar to a commercial bovine chymosin. These results indicate that P. pastoris expression system is very suitable for recombinant yak chymosin production to meet the needs of the cheese industry.