β-mannan is an abundant non-starch polysaccharide (NSP) in soybean meal (SBM) that elevates digesta viscosity and decreases nutrient utilization in fish. This research aimed to evaluate the impacts of graded levels of dietary β-mannanase (BM) supplementation on growth performance, digesta viscosity, digestive enzyme activity, short-chain fatty acids (SCFAs) production, gut histomorphometry, and microbiome composition in juvenile Nile tilapia, Oreochromis niloticus, fed SBM-based diets (440 g kg−1). From a control diet containing 19 MJ kg−1 gross energy, 311.2 g kg−1 crude protein and 71.3 g kg−1 crude lipids, five BM-supplemented diets were made adding liquid BM (Natupulse® TS, Basf, Ludwigshafen am Rhein, Germany Germany) at either 1600, 3200, 4800, 6400, and 8000 TMU (thermostable endo-1,4-BM units) kg−1 to the control diet. Fish were hand-fed six times a day to apparent satiety for 8 weeks. Each experimental diet was fed to quadruplicate groups of 21 fingerling Nile tilapia (initial weight of 7.0 ± 0.43 g) stocked in 70-L aquaria connected as a closed recirculating system. Based on quadratic regression analysis of body weight gain (BWG) the optimal dietary BM was estimated at 4821 TMU kg−1. Fish fed the diet with BM at 4800 TMU kg−1 showed higher feed efficiency ratio (P < 0.001), activity of amylase (P < 0.001; +12.7 μm g−1) and lipase (P < 0.001; +1.6 μm g−1) enzymes, and reduced digesta viscosity (P < 0.001; −0.88 cP (cP)) compared to fish fed the control diet. Additionally, dietary BM at 4800 TMU kg−1 also increased butyric acid content (P < 0.001; +0.31 nmol L−1), reduced gut pH (P < 0.001; −0.65), and increased villus height (VH; P < 0.001; +13.8 μm) relative to fish fed the control diet. Analysis of the “core microbiota” revealed that dietary BM modulated gut microbiota of juvenile Nile tilapia with fish fed the diet containing 4800 TMU kg−1 showing higher abundance of the beneficial bacteria, Proteobacteria, Actinobacteria, and Firmicutes, and a reduced population of potentially harmful bacteria (Escherichia sp.) than fish fed control diet. In summary, including BM at a level of ≥4800TMU kg−1 in SBM-based diets showed multiple beneficial effects on juvenile Nile tilapia growth performance, energy and nutrient utilization, and gut health, promoting improved gut histomorphometry and abundance of beneficial bacteria and reducing potentially harmful bacteria. These findings highlight the potential of BM supplementation as an advanced nutritional tool to enhance growth performance and gut health of juvenile Nile tilapia fed SBM-based diets.