Essential oils and organic acids have shown the potential to inhibit the proliferation of pathogenic bacteria and modulate the fish immune system. The present study evaluated the blend of protected essential oil and organic acids [P(EO+OA); AquaNat SynergyTM] in vitro against common pathogenic bacteria that afflict the catfish industry, and in vivo during a feeding trial using channel catfish juveniles. Minimum inhibitory and bactericidal concentrations (MIC and MIB) were established using the P(EO+OA) against Aeromonas hydrophila, Edwardsiella ictaluri, E. piscicida and Streptococcus iniae. Serial dilutions starting from the MIC values were tested with E. piscicida and A. hydrophila to assess biofilm formation, with Streptococcus iniae to evaluate hemolytic activity, and with E. ictaluri to quantify gene expression of virulent genes. Interestingly, concentrations lower than the MIC disrupted the normal metabolism of pathogenic bacteria by significantly reducing all the aforementioned parameters. The in vivo study evaluated the supplementation of the P(EO+OA) in diets for juvenile catfish at 0, 300, 600 and 1,500 mg/kg. A total of 840 channel catfish juveniles were equally distributed in 28 aquaria (30 fish/tank; n=7) operating as a recirculating aquaculture system. Fish were fed twice daily with rations corresponding to a percentage of the biomass, which was adjusted biweekly by group weighing each tank. The feeding trial was carried out for 124 days, and at the end of the study, production performance and condition indices were evaluated. Blood and intestine samples were collected for hematology, intestinal histology and expression of immune-related genes. Fish were fed their assigned experimental diets for an additional week and digesta from the posterior intestine were sampled 20 h post-feeding for DNA extraction and 16S rRNA gene sequencing on an Illumina MiSeq. The remaining fish from the feeding trial were subjected to a bacterial challenge by bath exposure using a LD50 dose of Edwardsiella ictaluri. No differences were observed for production performance, condition indices, expression of genes related to the antioxidant system from the intestine, and blood/plasma parameters. However, a lower expression of TNF-α and a higher expression of IL-6 was observed in the posterior intestine of fish fed P(EO+OA), 300 and 1,500 mg/kg respectively, when compared to the control group. No differences were observed for α- and β-diversity, but a higher relative abundances of bacteria from the genera Enterococcus and Romboutsia, and Plesiomonas, Weissella and Shewanella were observed in fish fed the 600 and 1,500 mg/kg of P(EO+OA) diets, respectively. In addition, a higher survivability was observed for fish fed 1,500 mg/kg of P(EO+OA) when compared to the control group after the E. ictaluri challenge. The commercial product AquaNat SynergyTM presented to be a promising feed additive for aquaculture by potentially decreasing virulence factors in vitro, as well as modulating the intestinal microbiota and immune-related genes of channel catfish juveniles during the feeding trial. In addition, highest dose of P(EO+OA) appeared to confer protection during the bacterial challenge, which shows potential to be applied in practical conditions as a prophylactic strategy when epizootic outbreaks are more likely to occur.