The present study aimed to investigate the metabolic fate and the cardiometabolic effects of phenolic compounds (PC) provided by a red‐fleshed apple variety biofortified in anthocyanins (ACN). Wistar rats were feed with high‐fat diet (HFD) to induce hypercholesterolemia and supplemented with red‐fleshed apple (HFD+R), white‐fleshed apple (HFD+W) or an ACN‐rich infusion from aronia fruit (HFD+A) providing matched content and profile of ACN. Plasma biochemical parameters, histological analysis and phenol biological metabolites were determined. Plasma, urine and faeces showed a significant increase of ACN metabolites after HFD+R and HFD+A, while flavan‐3‐ols were significantly increased after HFD+W and dihydrochalcones derivatives increased after both apples supplementation. A cardioprotective effect was observed after both apples and aronia infusion supplementation in the reduction of aortic thickness. The kidney function was improved after all supplementations and a decrease in insulin plasma concentration after both apples supplementation (HFD+R and HFD+W) was also observed. Our findings support that ACN without apple matrix can induce cardioprotective effects. ACN or flavan‐3‐ols, together with dihydrochalcones, compose a phenolic phytocomplex in red and white‐fleshed apples, respectively, that could act synergistically in the attenuation of cardiovascular outcomes in hypercholesterolemic rats.