Ultrafiltration (UF) of skimmed milk altered the composition of UF retentate and decreased the heat stability. Heat stability further reduced upon its subsequent homogenization or diafiltration. Poor heat stability of UF retentate restricts its processing at elevated temperatures. Therefore, this study was aimed to investigate the effect of protein concentration, homogenization and addition of stabilizing salts on the heat stability and rheological properties of UF retentates. Changes in the heat stability of fivefold homogenized UF retentate (5× HUFR) was studied in the pH range of 6.1–7.0. Disodium phosphate and trisodium citrate significantly increased the heat coagulation time (HCT) from 1.45 min (pH 6.41) to 120 min (at pH 6.5, 6.6, 7.0) and 80 min (pH 6.6), respectively. Significant reduction in ζ-potential of UF retentates was observed with an increase in calcium and reduction in pH during UF process. Rheological behaviour of retentates above threefold concentration exhibited Herschel–Bulkley behavior with linear increase in flow behavior index (n). Changes in the viscosity of the homogenized retentates were measured at the respective pH of maximum heat stability as a function of temperature (20–80 °C). Promising approaches that might improve the heat stability, solubility and other functional properties of protein rich powders have been discussed in this article.