The aim of the present study was to assess the effects of different flow-through heat treatments—68, 73, 78, 85, 100 °C for 16 s—applied to in-line homogenized goat and sheep milk. Alkaline phosphatase (ALP) activity in raw goat milk was 324.5 ± 47.3 μg phenol/mL, and that of lactoperoxidase (LPO) was 199.3 ± 6.7 U/L. The respective activities in raw sheep milk were 7615 ± 141 μg phenol/mL and 319 ± 38.6 U/L. LPO activity was not detected in both milk kinds treated at 85 °C for 16 s. Residual enzyme activities at 73 °C for 16 s with respect to the initial levels in raw milk were higher in goat than in sheep milk. The whey protein fraction of sheep milk was more heat sensitive compared to goat counterpart. Sheep milk rennet clotting time (RCT) was not affected by the treatments, while curd firmness decreased significantly (p < 0.05) at 100 °C for 16 s. Treatments more intense than 73 °C for 16 s increased the RCT of goat milk significantly but inconsistently and decreased curd firmness significantly, while yoghurt-type gels made from 73 °C or 78 °C for 16 s treated goat milk exhibited the highest water-holding capacity.
