This study investigated the synergistic effects of nanoemulsion of α-mangostin-rich extract (NEM) from mangosteen (Garcinia mangostana) pericarp and a natural free amino acid mixture (FAA) on growth performance, immune function, gene expression, digestive enzyme activity, intestinal morphology, gut microbiota, and disease resistance in Nile tilapia (Oreochromis niloticus). Over an 8-week feeding trial, 360 fish were divided into four dietary groups: control, NEM (10 g/kg), FAA (10 g/kg), and a combination of NEM + FAA (5 g/kg each). Fish fed the NEM + FAA diet exhibited significantly improved final body weight, weight gain, specific growth rate, feed conversion ratio, and fillet yield (P < 0.05). Enhanced serum biochemical parameters and elevated digestive and antioxidant enzymes activity were observed, along with significantly higher expression levels of growth- and immune-related genes (GH, GHR2, IGF-II, IL-1β, IL-6, IL-8). Histological analysis revealed improved intestinal villi height, muscularis thickness, and goblet cell density. Gut microbiota analysis showed increased diversity and beneficial shifts in microbial composition. Following Streptococcus agalactiae challenge, the NEM + FAA group achieved the highest survival rate (57.78 %) and relative percent survival (RPS = 47.22 %). These results suggest that the NEM + FAA combination enhances growth, immunity, and disease resistance, supporting its application as a functional dietary supplement for sustainable Nile tilapia aquaculture.