The effect of several purified phenolic compounds and green tea extract (GTE) on chymosin activity in model buffer solutions were found to be insignificant. The conserved secondary structure of chymosin upon interaction with phenolics, revealed by circular dichroism (CD) spectroscopy measurements, was considered to be the reason for unchanged enzyme activity. The coagulation properties of milk, however, was affected negatively by GTE addition. The RP-HPLC analysis and particle size measurements revealed that the caseinomacropeptide formation and aggregation of micelles was retarded in the presence of GTE during enzymatic coagulation of milk. The plasmin activity values during the ripening of miniature cheese samples were not affected by GTE addition while residual chymosin activity was decreased for cheeses fortified with GTE. Decreased levels of proteolysis of GTE-added cheese samples were observed with a 13–24% reduction in pH 4.6 SN/TN values, indicating a hindered primary proteolysis which was also confirmed by urea-PAGE and peptide profile analysis. The results of this study showed the importance of the interactions between phenolics and enzymes, as minor constituents of milk, for functional dairy product manufacturing.