Hypercaloric beverages increase the prevalence of insulin resistance and nonalcoholic fatty liver disease (NAFLD), diets with polyphenolic compounds improved these alterations. The study aimed to evaluate the effect of the consumption of three functional beverages (prepared with: Roselle, green tea, cinnamon, Malabar tamarind, and peppermint in different proportions) on insulin resistance and NAFLD and their relation to liver phospholipid regulation in Wistar rats fed with a high‐fat and fructose (HFF) diet. The consumption of beverages showed lower liver triglycerides compared to HFF control group, being the called beverage B the successful triggering up to 30.1%. The consumption of functional beverages improved insulin resistance and decreased the abundance of LysoPC (20:2), LysoPC (16:0), LysoPC (14:0), LysoPE (18:0), LysoPC (15:0), and LysoPC (20:1), with beverage C being the one with the meaningful effect. The results indicate that the functional beverage consumption improves insulin resistance, and decrease the degree of NAFLD, these through modifications of lysophosphatidylcholines, and lipids metabolism.