Abstract Background Inflammatory bowel disease (IBD) is characterised by chronic, relapsing intestinal inflammation with extensive damage of the colonic mucosa and a remarkable dysbiosis. Since the current treatments show limitations in the response of some patients and many of them are associated with important side effects, new and safer strategies are needed. Postbiotics are any soluble factor resulting from the metabolic activity of a live probiotic bacteria or any released molecule capable of providing health benefits through a direct or indirect mechanism. Nevertheless, the effects of certain postbiotics in the context of intestinal inflammation have not been extensively addressed. Our aim is to study the immunomodulatory properties of two different postbiotics on primary human cell culture and their protective effects on human intestinal ex vivo 2D culture. Methods Postbiotics from Streptococcus salivarius subsp. thermophilus and Lactobacillus paracasei Lpc-37 were obtained after the microbial culture of each bacterial strain. Supernatants were collected at OD600 = 0.6, filtered and frozen. Immunostimulatory, immunosuppressor or immunomodulatory effects of each postbiotic were tested in peripheral blood mononuclear cells (PBMCs) isolated from healthy donors (n = 4). PBMCs are a heterogenous cell population that includes myeloid as well as lymphoid immune cells. Postbiotics were used to assess whether bacterial metabolites could modulate the cytokine release in particular IL-12p40 and IL-10 by LPS-stimulated PBMC, mimicking innate immune activation. Dendritic cells (DCs) differentiated from isolated human monocytes were also stimulated with all postbiotics (n = 2) to study the innate-adaptive immune crosstalk by analyzing IL-10 and IL-12p70 secretion. Postbiotics stimulation was also performed in differentiated human intestinal epithelial monolayers derived from EpOCs (Epithelial Intestinal Organoids Cells) to analyse the outcome in an ex vivo organ culture. Results Postbiotics derived from S.thermophilus and Lpc-37 were able to increase the secretion of IL10 in both PBMCs and monocyte-derived DCs, while no change was shown in IL-12p40/IL-12p70 production. Interestingly, S. thermophilus also showed a ‘per se’ anti-inflammatory effect due to an increase of IL-10 in non-stimulated PBMCs. On the other hand, postbiotics were able to up-regulate MUC2 expression in the 2D organ culture while down-regulating LGR5. Conclusion Overall we conclude that the tested postbiotics show an immunomodulatory effect as well as important properties on intestinal epithelial-cells stemness and differentiation, being S. thermophilus the best candidate due to its remarkable anti-inflammatory effect in both stimulated and non-stimulated cells.