Thermal processing constitutes the principal intervention for controlling microbiological hazards in dairy manufacturing; however, its interaction with the nutritional matrix of fermented products remains incompletely characterised. This study investigates the combined effect of pasteurisation regimes on the microbiological safety profile and biological value of kurt — a traditional Central Asian hard-dried yoghurt — as well as the nutritional potential of the whey by-product generated during its production. Physicochemical, microbiological and amino acid analyses were conducted on control and heat-treated kurt samples alongside the resulting whey fractions. Results demonstrate that high-temperature short-time (HTST) pasteurisation at 72 °C for 15 seconds achieves a 5-log reduction in total mesophilic aerobic counts while preserving 94.3 ± 1.2% of total protein content and 91.7 ± 1.6% of lysine bioavailability. Whey recovered from kurt processing contained 13.8 g·100 g⁻¹ protein, 4.6 g·100 g⁻¹ lactose and appreciable levels of calcium (112 mg·100 g⁻¹), qualifying it as a substrate for functional beverage formulation. A protein drink designated "qurtoba", incorporating kurt concentrate and cold-pressed pumpkin seed extract, yielded a Protein Digestibility-Corrected Amino Acid Score (PDCAAS) of 0.88 and demonstrated superior antioxidant capacity (DPPH inhibition: 68.4%) relative to the whey baseline. These findings provide quantitative evidence that optimised thermal processing can reconcile microbiological safety requirements with nutritional retention and support sustainable zero-waste valorisation of dairy by-products.