In this study, the effect of supplementation of low fat bovine milk with whey protein concentrates (WPC) or whey protein hydrolysates (WPH) on the biofunctional and rheological properties of the produced yoghurt was assessed. Six different set type yoghurt products containing 1.6% fat were manufactured and enriched with: a) 1.5% bovine WPC (80% protein), marked as WPC_A yoghurt, b) 1% WPC (80% protein) of ovine/caprine origin, marked as WPC_B yoghurt, c) 2% commercial mixture of milk proteins, i.e. milk protein concentrate/ caseinates /WPC  (82% total protein content), marked as MPM yoghurt, d) 0.25% WPC_B hydrolysed with trypsin, marked as WPH_A yoghurt, e) 0.5% commercial WPH, marked as WPH_B1yoghurt, f) 0.25% commercial WPH, marked as WPH_B2 yoghurt. Control yoghurt was manufactured without addition of protein. Results showed that the protein fortification level affected positively the protein, total solids as well as calcium and phosphorous contents of all yoghurt types. The lowest pH values were observed in the case of WPH_B2 yoghurt, while the highest in the case of MPM yoghurt throughout the storage i.e. 21 days. The characteristic microorganisms were in total more than 10⁸cfu/g. Yoghurts fortified with WPH showed higher ACE-inhibitory activity (determined by the HPLC method) than those enriched with WPC. Also, it is noteworthy that WPH_A yoghurt showed significantly (P<0.05) higher ACE-inhibitory activity (72%) than control yoghurt or yoghurts made with the other WPH. On the other hand, WPH_A yoghurt showed the lowest hardness and adhesiveness, whereas MPM yoghurt showed the highest. The type of added whey protein did not affect cohesiveness. Water holding capacity was higher in yoghurts enriched with WPC and MPM than in the yoghurts enriched with WPH. All yoghurts presented antioxidant activity such as DPPH^• radical scavenging activity (45-58%). The WPC_A yoghurt, MPM yoghurt, WPH_A yoghurt and control yoghurt presented high Fe²⁺ chelating activity (>70%), but WPH_A yoghurt presented the highest Fe²⁺ chelating activity (>95%) throughout storage.  In conclusion, fortification of yoghurt milk with WPH increased the biofunctionality of the product, but the use of WPH of ovine/caprine origin increased it significantly.