Nanotechnology can enhance nutrient delivery and bioavailability; hence, it has recently been considered the most practical alternative technology for nutritional supplements and disease control in fish farming. The present study was designed to evaluate the effects of mangosteen peel extract loaded in nanoemulsion (MSNE) on the inhibition of A. veronii (in vitro) and in vivo growth performance, serum biochemical parameters, the immune response, and the disease resistance of Nile tilapia (Oreochromis niloticus) against A. veronii challenge. The particle size, polydispersity index, and particle surface charge of MSNE were 151.9 ± 1.4 nm, >0.3, and −30 mV, respectively. Furthermore, MSNE, mangosteen peel extract (MPE), and nanoemulsion (NE) improved the antimicrobial activity against A. veronii. Fish fed MSNE, MPE, and NE-supplemented diets had a significantly lower (p < 0.05) feed conversion ratio (FCR) and higher specific growth rate (SGR) than fish fed the control diet. Furthermore, the MSNE had significantly higher serum glucose and protein levels than the control group in Nile tilapia. Total immunoglobulin, serum lysozyme, alternative complement activity, and survival of Nile tilapia fed with MSNE were significantly higher (p < 0.05) than the control diet. Therefore, MSNE has the potential to be employed as a supplement in sustainable Nile tilapia farming.