Chia is a functional food because of its positive impact on reducing the risk of metabolic diseases. These benefits are due to its nutritional composition as a source of dietary fiber and bioactive compounds. In our previous study, chia consumption increased the richness of the microbiota and the production of short chain fatty acids (SCFAs) when consumed by male Wistar rats, so, the objective of this study was to assess the effects of the consumption of chia with a high fat diet on gut health in female Wistar rats. 32 adult female Wistar rats were allocated into four groups and received one of the following diets: standard diet (SD), standard diet + chia (SDC), high fat diet (HFD) or high fat diet + chia (HFDC) for 8 weeks. At the end of the study, the intestinal microbiota, SCFA content, cecum content pH, immunoglobulin A (IgA) quantification and brush border membrane functionality were evaluated. There was no difference in the relative abundance of the gut microbiota, but chia consumption increased the microbial richness and diversity, increased the production of acetic and butyric acids in the SDC group and propionic acid in the HFD group, and decreased the pH of cecal content. The HFDC group demonstrated a lower IgA concentration compared to the HFD group. The SDC group increased SI and AP gene expression and decreased SGLT1 and PepT1 compared to the SD group. The consumption of chia can be beneficial for the functionality of the microbiota, improving SCFAs and intestinal pH, and the effects of chia in the microbiota can be more pronounced in HFD.