Finfish and fish products are globally the most acknowledged health-promoting foods. The rising incidence of pathogenic and disease outbreaks have had a sizeable impact on aquaculture. Microbial supplementation of food in the form of probiotics, prebiotics, and their controlled release combinations (=co-encapsulations) as ‘synbiotics’ is noted for its significant biotherapeutic and health benefits. Supplementation of probiotic microbial feed additives in the fish diet claims to improve fish health by modulation of resident intestinal microbiota and by introducing healthy microbiota procured from an exogenous source, capable of combating pathogens, improving nutrient uptake, assimilation, growth as well as survival. Prebiotics are selectively digestible substrates beneficially used by host gut microbes to enhance probiotic effects. Formulating a fish diet with augmented probiotics and prebiotic microbial bio-supplements can ensure a sustainable alternative for establishing fish health in a naturally susceptible aquaculture scenario. Micro-encapsulation, co-encapsulation, and nano-encapsulation are novel strategies of biotechnical interventions in functional feeds for finfish. These aim to improve probiotic persistence, survivability, and efficacy in commercial formulations during probiotic transit through the host-gut environment. This review discusses the importance of co-treatment and encapsulation strategies for improving probiotic and prebiotic potential in aquafeed formulations, reliably improving finfish health and nutritional returns from aquaculture, and, consequently, for consumers.