Lactic acid bacteria (LAB) are key players in the fermentation of organic wastes and their recycling as feedstuff for fish. Whey, a common dairy byproduct in India, is a cheap source of LAB and can be used to ferment animal byproducts. An experimental study was designed to explore whether the whey fermented animal protein blend (WFAPB) could be used as a fishmeal replacer in the formulation of feed for both stomach-less carp fish Labeo rohita and stomach-bearing catfish Mystus vittatus. Experiments were performed with five isoproteinous, isolipidous, and isoenergetic feeds with WFAPB replacing fishmeal (FM) by 0% (T1), 25% (T2), 50% (T3), 75% (T4), and 100% (T5). Fifteen days of laboratory experiments with these experimental feeds revealed that more than 50% FM replacement level could result in excess postprandial absorption (6 h) of some essential and non-essential amino acids in the plasma of both fish. The postprandial absorption was more in M. vittatus than L. rohita. Ninety-day experiments were conducted in outdoor cement vats to measure growths and deposition of amino acids (AA) in muscle. Regression analysis was performed to find the optimal FM replacement based on four growth parameters and fifteen AA deposition in muscle. A two-phase fuzzy methodology was used to obtain Pareto-optimal replacement levels for each fish. The results demonstrated that FM replacement levels were 7.63% and 36.79% respectively for L. rohita and M. vittatus when only four growth parameters were considered. However, based on the FM replacement level that maximized deposition of 15 amino acids and growth parameters, it was found that 12.23% and 40.02% replacement of FM by the WFAPB was ideal respectively for L. rohita and M. vittatus. The results revealed that only a fraction of both essential and non-essential amino acids absorbed in plasma could be converted into protein and deposited as bound amino acids in the muscle. It is concluded that fermentation by whey is an inexpensive, easily available, and environmentally sustainable technique to recycle animal protein in the formulation of feed for fish, and the stomach-bearing carnivorous fish are more efficient in utilizing fermented animal protein blend than the stomach-less carps.