The effect of homogenization and fat reduction in combination with variable heating conditions of cow milk on the characteristics of Quark-type cheese were investigated. The mean composition of full-fat cheeses was 71.96% moisture, 13.95% fat, and 10.31% protein, and that of its reduced-fat counterparts was 73.08%, 10.39%, and 12.84%, respectively. The increase of heat treatment intensity increased moisture retention and improved the mean cheese protein-to-fat ratio from 0.92 to 1. Homogenization increased the moisture and protein retention in cheese, but the effect was less intense for milk treated at 90 °C for 5 min. The extended denaturation of whey proteins resulted in harder, springier, and less cohesive cheese (p < 0.05). Treatment of milk at 90 °C for 5 min resulted in higher residual lactose and citric acid and lower water-soluble nitrogen contents of cheese (p < 0.05); the latter was also true for homogenization (p < 0.05). Storage did not affect the composition and texture but decreased galactose and increased citric acid and soluble nitrogen fractions (p < 0.05). In conclusion, heat treatment conditions of milk that induced a considerable denaturation of β-lactoglobulin and left a considerable amount of native α-lactalbumin was adequate for the manufacture of a “clean-label” Quark-type cheese, whereas homogenization was more effective for full-fat cheese.