The increasing reliance on fishmeal as a primary protein source in aquaculture feeds has raised major concerns related to sustainability, rising production costs, and environmental degradation. Consequently, plant-based protein sources have gained considerable attention as viable alternatives for fishmeal replacement. However, high inclusion levels of plant-derived ingredients are frequently associated with reduced nutrient digestibility, disruption of intestinal microbial balance, and increased susceptibility to pathogenic infections, thereby limiting the efficiency of fishmeal replacement strategies in intensive aquaculture systems. Microbial biocontrol has emerged as a sustainable and biologically driven approach to address these limitations associated with alternative feed formulations. Beneficial microorganisms, including probiotics and gut-associated microbiota, play a crucial role in maintaining intestinal homeostasis, enhancing digestive enzyme activity, and suppressing opportunistic pathogens through competitive exclusion, antimicrobial metabolite production, and host immune modulation. In addition, microbial fermentation of plant-based feed ingredients has been shown to reduce anti-nutritional factors, improve feed palatability, and enhance nutrient bioavailability, thereby supporting growth performance and overall fish health under reduced-fishmeal diets. This review critically examines the synergistic interactions between plant-based fishmeal replacement strategies and microbial biocontrol mechanisms in sustainable aquaculture. Emphasis is placed on microbial interventions that improve feed utilization efficiency, enhance disease resistance, and reduce dependence on antibiotics and chemotherapeutics. Current challenges, recent advances, and future research perspectives are also discussed to support the development of environmentally responsible and resilient aquaculture practices.