Background Salmonella enterica serovar Pullorum, the causative agent of pullorum disease, is one cause of the economic losses in the global poultry industry. Vaccination and antibiotics are still the most effective methods of controlling Salmonella, even though the vaccine contains the causative agent, and the antibiotic therapy has limited efficacy. We provide a novel immunostimulator and antibiotic substitute to protect against and avoid Salmonella pullorum (SP) infection. Methods Nigella sativa-purified oil (NS) and monophosphoryl lipid A (MPLA) were formulated as nanoliposomal compounds (NS-MPLA). Their protective and immunomodulatory efficacies were experimentally tested orally in broiler chicks against challenge with virulent pandemic drug-resistant SP. Four chick groups were utilized: control; NS-MPLA-supplemented; SP-challenged; and SP-challenged, then NS-MPLA-treated. Clinical signs, organ gross pathology, colony-forming counts, and tissue histopathological alterations were investigated. The relative fold-changes in the expression of IL-1β, IL-4, IL-17, IL-22, TLR-4, INF-γ, IgA, and MUC2 genes were evaluated. Results The SP-challenged chicks showed notable symptoms and extensive pathological lesions in their internal organs. The bacteria colonized the challenged chicks' livers and continued to shed in their feces for 5–6 days. A minor amount of immune cell tissue trafficking was noted. The NS-MPLA-treated chicks displayed opposing patterns after being challenged with SP. They exhibited mild clinical signs with modest gross pathology in the internal organs. After 3–4 days, the liver and the fecal droppings were cleared of SP. Significant heterophilic aggregation, lymphocytic infiltration, and lymphoid follicle enlargement were observed. Additionally, chicks challenged with SP and then NS-MPLA-treated showed a 5- to tenfold increase in immune-related cytokines, immunoglobulin A, and mucosal relative gene expression folds compared to the SP-challenged non-NS-MPLA-treated, which showed a sharp decline in IL-4 and IL-22 and a minor rise in the rest of the tested gene relative expressions. Chicks given NS-MPLA supplementation showed a significant upregulation of these genes compared to the control group. Conclusion In this first report on poultry, it is possible to draw the conclusion that NS-MPLA supplementation in SP-infected chicks boosts immunity and provides protection. It promoted bacterial clearance and tissue repair and stimulated the expression of genes linked to immunity and the mucosal surface. These findings suggest the potential application of NS-MPLA in salmonella control programs as an antibiotic substitute or in immunization strategies.