The processing of strained yogurts, and fresh cheeses, such as ricotta or cottage, generates large amounts of waste streams known as acid whey (AW) that require significant capital investments for proper disposal. Similarly, the fishery industry produces about 45% of the whole fish as waste at the end of its production chain. To valorize these by-products, this study is based on the hypothesis that fermentation of the mixture of AW and fish waste (FW) would break down complex nutrients, increasing its nutritional value for aquaculture. The objective of this study was to optimize fermentation parameters using lactic acid bacteria (LAB) and a mixture of AW and FW. The first step was screening of the LAB in the OSU “Parker Chair” LAB Collection to identify the strain with the highest proteolytic activity. Then, 3 fermentation systems (FS) were inoculated with Lactobacillus rhamnosus and set up as follows: 1) FS1: 36% FW, 12% fish muscle, 48% AW, and 4% molasses; 2) FS2: 38% FW, 12% fish muscle, and 50% AW; 3) FS3: 48% FW, 48% AW, and 4% molasses. The fermentation lasted 14 d at room temperature, and samples were collected every 48 h. The soluble protein concentration and peptide concentration of the samples were evaluated with colorimetric assays (Bradford and cadmium-ninhydrin), SDS-PAGE, pH, and microbial count of LAB was monitored simultaneously. The results showed a significant increase (P < 0.05) of peptides over time in the 3 fermentation systems. However, FS2 had 3.6 times more peptides than that of day zero’s, and the values of Bradford and SDS-PAGE images were consistent with the results presented in the peptide assay. The pH dropped significantly (P < 0.05) from 5.88 to 4.09 for FS1 and FS3 on the first 6 d due to the content of molasses and lactic acid production. Conversely, FS2 had a significant increase from 5.96 to 7.07. The LAB count fluctuated within each fermentation system and over the 14 d. In conclusion, this study presents an alternative to the current handling of acid whey and fish waste, exploiting their residual nutrients for delivery of higher quality protein to animal diets with minimal treatment.