In recent years, research has explored use of microfiltered (MF) milk for cheesemaking. The goal of this study was to determine if the amount of whey protein (WP) depleted from cheesemilk via MF affects the amount of residual WP in cheese as well as functionality and quality. Casein content for all milks was kept at 2.5% to eliminate the confounding factor of casein concentration. Three standardized cheesemilks were made with varied casein:true protein (CN:TP) ratios: (a) control with a CN:TP ratio of 0.83, (b) 35% WP depletion, 0.89 CN:TP, and (c) 70% WP depletion, 0.95 CN:TP. Standardized cheesemilks were analyzed for chemical composition. Cheddar cheeses were aged for 9 mo and composition and functionality were evaluated at 4 d, 2 wks, 1 mo, 3, 6, and 9 mo. Cheese yield, solids recovery, and nitrogen recovery were highest in the 70% WP depleted cheese followed by the 35% WP depleted and control, respectively. Because WP are mostly lost in whey drainage steps of cheesemaking, depletion of WP from the starting cheesemilk improves cheesemaking efficiency (i.e., less of the proteins/solids in cheesemilk are lost). Rheological properties of cheeses were monitored by small-strain oscillatory testing while heating to 85°C. Residual WP content of cheese decreased with increasing MF depletion displaying the effectiveness of MF treatment. The maximum loss tangent (LT_max), an index of meltability, was highest at all time points in the 70% WP depleted cheese followed by 35% WP depleted and control, respectively. LT_max also increased with ripening for all cheeses. At 1 mo, the temperature at which the LT_max occurred was highest in the control cheese followed by 35 and 70% WP depleted samples, respectively. The LT_max values increased with age for all cheeses while the LT_max temperature decreased. It is possible that residual WP maybe inhibiting proteolysis during ripening. Hardness decreased with age for all cheeses due to proteolytic activity. MF treatment did not affect sensory attributes. Depletion of WP in cheesemilk by MF did not negatively affects quality but resulted in improved cheese efficiency.