Recent studies have demonstrated that immune-related recombinant proteins can enhance immune function, increasing host survival against infectious diseases in salmonids. This research evaluated inclusion bodies (IBs) of antimicrobial peptides (CAMP^IB and HAMP^IB) and a cytokine (IL1β^IB and TNFα^IB) as potential immunostimulants in farmed salmonids. For this purpose, we produced five IBs (including iRFP^IB as a control), and we evaluated their ability to modulate immune marker gene expression of three IBs in the RTS11 cell line by RT–qPCR. Additionally, we characterized the scale-up of IBs production by comparing two different scale systems. The results showed that CAMP^IB can increase the upregulation of tnfα, il1β, il8, and il10, HAMP^IB significantly increases the upregulation of tnfα, inos, and il10, and IL1β^IB significantly upregulated the expression of tnfα, il1β, and cox2. A comparison of IL1β^IB production showed that the yield was greater in shake flasks than in bioreactors (39 ± 1.15 mg/L and 14.5 ± 4.08 mg/L), and larger nanoparticles were produced in shake flasks (540 ± 129 nm and 427 ± 134 nm, p < 0.0001, respectively). However, compared with its shake flask counterpart, the IL1β^IB produced in a bioreactor has an increased immunomodulatory ability. Further studies are needed to understand the immune response pathways activated by IBs and the optimal production conditions in bioreactors, such as a defined medium, fed-batch production, and mechanical bacterial lysis, to increase yield.