Type 2 Diabetes (T2D) is a major health problem worldwide. It has been shown that subjects with T2D present dysbiosis in the intestinal microbiota. Functional foods can be considered as dietary strategy to the control of some chronic diseases related to nutrition. The purpose of the present work was to evaluate the combination of functional foods (FF) (nopal, oats, chia seed and inulin) on biochemical parameters and changes in the gut microbiota. A double‐blind randomized clinical trial compared to placebo was performed. The intervention with FF was accompanied by an eating plan according to the guidelines of the American Diabetes Association by 3 months. Blood and feces samples were collected before and after the dietary intervention. DNA from feces was extracted for 16S ribosomal gene sequencing using the MiSeq plataform. The results of the present study showed that the T2D gut microbiota was significantly different from healthy subjects. The predominant species in T2D subjects were Helicobacter apodemus, Bacteroides fragilis, Bacteroides plebeius , Colinsella erofaciens and Muciprillum schaedleri , and there was a reduction of species such as Akkermansia muciniphila and Faecalibacter prausnitzii compared to healthy subjects. After the intervention with functional foods (FF), we observed a significant increase in Faecalibacterium prausnitzii (placebo 14% vs FF 42%), R bromi (placebo 45% vs FF 562%), and a reduction in B uniformis (placebo −22.7 vs FF −45.3%). Finally, there was a significant reduction in serum glucose triglycerides, lipopolysaccharide, and HbA1c in T2D subjects that consumed FF with respect to the placebo group. Support or Funding Information Grant CONACYT 261079 (to NT).