Intestinal disorders can affect pigs of any age, especially when animals are young and more susceptible to infections and environmental stressors. For instance, pathogenic E. coli can alter intestinal functions, thus leading to altered nutrient adsorption by interacting with local cells through lipopolysaccharide (LPS). Among several compounds studied to counteract the negative effects on the intestine, short-chain fatty acids (SCFA) were demonstrated to exert beneficial effects on gut epithelial cells and resident immune cells. In this study, acetate and propionate were tested for their beneficial effects in a co-culture model of IPEC-J2 and porcine PBMC pre-stimulated with LPS from E. coli 0111:B4 aimed at mimicking the interaction between intestinal cells and immune cells in an inflammatory/activated status. IPEC-J2 viability was partially reduced when co-cultured with activated PBMC and nitric oxide concentration increased. IPEC-J2 up-regulated innate and inflammatory markers, namely BD-1, TLR-4, IL-8, TNF-α, NF-κB, and TGF-β. Acetate and propionate positively modulated the inflammatory condition by sustaining cell viability, reducing the oxidative stress, and down-regulating the expression of inflammatory mediators. TNF-α expression and secretion showed an opposite effect in IPEC-J2 depending on the extent of LPS stimulation of PBMC and TGF-β modulation. Therefore, SCFA proved to mediate a differential effect depending on the degree and duration of inflammation. The expression of the tight junction proteins (TJp) claudin-4 and zonula occludens-1 was up-regulated by LPS while SCFA influenced TJp with a different kinetics depending on PBMC stimulation. The co-culture model of IPEC-J2 and LPS-activated PBMC proved to be feasible to address the modulation of markers related to anti-bacterial immunity and inflammation, and intestinal epithelial barrier integrity, which are involved in the in vivo responsiveness and plasticity to infections.