In recent times, nutraceuticals have been used extensively to identify promising feed additives for the improvement of the aquaculture industry through the enhancement of growth and survival rates, potentiation of the immune responses, and fortification of the resistance against infectious bacterial diseases. In this study, Nile tilapia (Oreochromis niloticus) were fed with diets supplemented with quinoa seeds (QU) or prickly pear fruit peel (PP) at the dose levels of 10% or 20% of the diet. After 45 days of the feeding trial, the fish were exposed to Aeromonas sobria (A. sobria) challenge. The pre-challenge indices indicated that both supplements mediated a significant improvement in most of the estimated parameters, including survival rate, antioxidant status, hematological and immunological indices, and hepatoprotective potential. These effects were recorded in the groups fed with high doses of the supplements (20%). The least changes were observed in the QU10-supplemented fish. In the spleen tissue, the TGF-β gene was upregulated in the PP10-, PP20- and QU20-supplemented groups, while the expression of the IFN-γ gene remained unaffected in all the supplemented groups, except for the PP20-supplemented group, which showed an upregulation. After the challenge with A. sobria, the relative survival percentage was improved by the supplementation of PP and QU, particularly in the PP20-supplemented group, possibly via the promotion of immunological responses, hepatoprotective potency, and modulation of the studied genes. Moreover, the morphological structure of the tissues showed marked recovery. The findings suggest that Nile tilapia fed with different levels of PP peel and QU seeds, particularly at the level of 20%, enhanced the immune response in fish and improved their resistance against A. sobria infection.