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Probiotics as antibiotic alternatives for preventing and controlling infectious diseases are a relatively eco-friendly strategy in aquaculture. The bacteriocin-producing probiotic <i>Paenibacillus ehimensis</i> NPUST1 was isolated from tilapia culture pond water in our previous study. The present study demonstrated that <i>P. ehimensis</i> NPUST1 produced hydrolytic enzymes, including protease, amylase, cellulase, xylanase and lipase. The effects of <i>P. ehimensis</i> NPUST1 on zebrafish nutrient metabolism, growth performance and innate immunity were evaluated by measuring the expression of indicator genes in zebrafish after feeding <i>P. ehimensis</i> NPUST1 at doses of 10⁶ and 10⁷ CFU/g for 8 weeks. There was an obvious increase in the hepatic mRNA expression of carbohydrate metabolism-related genes, including glucokinase, hexokinase 1, glucose-6-phosphatase, and pyruvate kinase, and growth-related genes, including the growth hormone receptor and insulin-like growth factor-1. The expression of the innate immune-related genes including interleukin (IL)-1β, IL-6, IL-15, tumor necrosis factor-α, toll-like receptor (TLR)-1, TLR-4, complement component C3b and lysozyme were significantly increased in <i>P. ehimensis</i> NPUST1-supplemented fish. A significant reduction in cumulative mortality was exhibited in <i>P. ehimensis</i> NPUST1-supplemented fish after infection with <i>Aeromonas hydrophila</i> and <i>Streptococcus iniae</i>. In conclusion, our data suggested that <i>P. ehimensis</i> NPUST1 supplementation in feed could potentially improve nutrient metabolism and growth in addition to enhancing innate immunity and disease resistance against <i>A. hydrophila</i> and <i>S. iniae</i> in zebrafish.