The production of Greek and Greek style yogurt (GSY) generates large amounts of an environmentally harmful waste product known as acid whey. Because disposal of this waste product is an expensive process, the Greek yogurt industry is searching for a solution to decrease the production of acid whey. The purpose of this study was thus to investigate the effects of pectin and whey protein concentrate (WPC) on the generation of acid whey during GSY production. Acid whey production was measured by calculating the water holding capacity (WHC). First, pectin (0.05%) and WPC (1%) were added to skim milk for the production of GSY. The yogurt mixes were then heated at 90°C for 10 min, inoculated with 3.0% of starter culture, incubated at 40°C for 4 h (pH ~4.6), and then refrigerated overnight at 5°C. A control yogurt sample was prepared without the addition of these ingredients. The yogurt made with pectin and WPC had a significantly higher WHC (P < 0.05) and lower syneresis than the control. The WHC of yogurt with both pectin and WPC was ~56%, which was 23% higher than the control (33%). Similarly, yogurt supplemented with both pectin and WPC exhibited 15% less susceptibility to syneresis compared with the control. Native PAGE analysis revealed an interaction between pectin and the WPC. Pectin hinders the formation of large oligomeric aggregates of whey protein, which correlates with an increase in WHC and a decrease in syneresis. Our results demonstrated that ingredients such pectin and WPC could be used as additives to lower the generation of acid whey in the production of Greek style yogurt.