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Scope The consumption of two healthy diets (Mediterranean (MED) and low‐fat (LF) diets) may restore the gut microbiome dysbiosis in obese patients depending on the degree of metabolic dysfunction. Methods and results The differences in bacterial community at baseline and after 2 years of dietary intervention of 106 subjects from the CORDIOPREV study were analyzed, 33 of whom were obese patients with severe metabolic disease (5 criteria for metabolic syndrome) (MetS‐OB), 32 obese patients without metabolic dysfunction (2 or less criteria for metabolic syndrome) (NonMetS‐OB) and 41 non‐obese subjects (NonMetS‐NonOB). Our study showed a marked dysbiosis in people with severe metabolic disease (Met‐OB), compared with obese people without MetS (NonMetS‐OB) and non‐obese people (NonMetS‐NonOB). This disbiotic pattern was reversed by consumption of both MED (35% of calories as fat (22% MUFA fat, 6% PUFA fat and <10% saturated fat) or LF (<30% total fat (<10% saturated fat, 12%–14% MUFA fat and 6–8% PUFA fat) diets, whereas no significant microbiota changes were observed in NonMetS‐NonOB and NonMetS‐OB groups. Conclusion Our results suggest that the chronic intake of two healthy dietary patterns partially restores the gut microbiome dysbiosis in obese patients with coronary heart disease, depending on the degree of metabolic dysfunction.