Goat (GCW) and sheep cheese whey (SCW) are cheese by-products that can be fermented to develop a new product. However, the limited nutrient availability for lactic acid bacteria (LAB) growth and the low stability of whey are challenges. This work evaluated the addition of protease and/or ultrasound-assisted fermentation as tools to improve GCW and SCW fermentation and the final quality of the products. Results showed that the US/protease increased by 23–32% pH decline rate (for SCW only) and modified the separation of cream (≤ 60% for GCW) and whey (≤ 80% for both whey sources, with higher values for GCW) during storage, explained by changes in the microstructure protein, fat globules, and their interactions. Furthermore, the whey source/composition (mainly lower fat content in SCW) affected the destabilization rate and the LAB viability loss (1.5–3.0 log CFU/mL), caused by nutrient depletion and low tolerance at pH ~ 4.0. Finally, exploratory results showed that fermentation under sonication (with/without protease) resulted in 24–218% higher antioxidant activity in vitro than unfermented samples. Therefore, fermentation associated with proteases/sonication can be an interesting strategy to modify GWC and SCW, and the final process chosen depends on the desired changes in whey.