Identifying novel natural sources from the marine environment with unique immunomodulatory and antioxidant efficacies is of interest in intensive fish farming. In this sense, marine sponge extract derived from Smenospongia (SS-extract) was tested for its potential anti-inflammatory, antioxidant and antimicrobial activities during the concurrent infection with Trichodina sp. and Flavobacterium columnare in Nile tilapia. A total of 625 Nile tilapia fingerlings were distributed into five groups: the control group (with no additives) and four groups fed the control diet fortified with SS-extract at 50, 100, 150, and 200 mg/kg, respectively, for 60 days. The parasitic challenge with Trichodina sp was done at the endpoint of the feeding trial and at 7 days post-infection (dpi); the fish were coinfected with F. columnare. A significant improvement in growth-related parameters of Nile tilapia was detected in the groups that received SS-extract at the levels of 150 and 200 mg/kg. The scavenging ability for free radicals (2,2′-azino-bis-3-ethylbenzthiazoline-6-sulfonic acid (ABTS) and 2,2-diphenyl-1-picrylhydrazyl (DPPH)) was maximized with higher SS-extract supplementation levels. Simultaneously, the antioxidant defense of the Nile tilapia fed 150 and 200 mg/kg was augmented with a decline in oxidation-associated indicators [reactive oxygen species (ROS), hydrogen peroxide (H2O2), and malondialdehyde (MDA)]. The higher concentrations of SS-extract in the feed potentiated the immune response of Nile tilapia before infection and even after coinfection and was paralleled by a subsiding in the exaggerated inflammatory response after concurrent infection. Concurrently, the mRNA expression of autophagy-encountered genes (Atg5 and 12, LC3-II and BCLN1) had its highest expression in the fish fed the 200 mg/kg diet with the lowest expression of the mTOR gene in the same fish. The lowest infection intensity and rate and mucus score were displayed in fish fed 200 mg/kg SS-extract at 20 dpi. Interestingly, higher levels of SS-extract triggered antimicrobial peptides (upregulation of Hepcidin and β-defensin-1). In contrast, excessive expression of endoplasmic reticulum genes (atf4, JAK1, PERK, and eif2α) in the control infected group was downregulated by 200 mg/kg of SS-extract. The quantification of F. columnare indicated that columnaris coinfection severity displayed its lowest rate in the group supplemented with 200 mg/kg of SS-extract. In conclusion, a strategic siting based on fortification of the diet of Nile tilapia with SS-extract was elucidated to reinforce its immune and antioxidant defenses during a concurrent infection.