Acidified dairy products generate large amounts of waste called acid whey (Aw). Similarly, the fishery industry wastes 45% of the whole fish by the end of its production chain. To valorize these by-products, this study hypothesized that fermentation of Aw and fish waste (Fw) would break down complex nutrients, increasing its bioavailability. The objective of this study was to optimize fermentation parameters using lactic acid bacteria (LAB) and a mixture of Aw, Fw, and molasses (Mol). Two fermentation systems were inoculated with Lactobacillus rhamnosus and set up as follows: 1) Fw+Aw; 2) Fw+Aw+Mol. The fermentation lasted 14 days at room temperature, and samples were collected every 48 hours. Soluble protein concentration and peptide concentration were evaluated with colorimetric assays, Bradford and cadmium-ninhydrin respectively; SDS-PAGE, pH, and microbial count of LAB were monitored simultaneously. The results showed a significant increase (P<0.05) of peptides over time in the fermentation systems. However, fermentation 2 had 3.6 times more peptides at day 14 than that of day zeroâ€™s, and the values of Bradford and SDS-PAGE images were consistent with the peptide assay. The pH dropped significantly (P<0.05) from 5.88 to 4.09 in the first six days due to the Mol. Conversely, fermentation 1 had a significant increase from 5.96 to 7.07. The LAB count fluctuated within each fermentation system and over time. In conclusion, this study presents an alternative to the current handling of Aw and Fw, exploiting their residual nutrients for the delivery of higher quality protein to animal diets with minimal treatment.