The regular consumption of dealcoholized red wine (DRW) has demonstrated benefits in cardiovascular risk factors. The analysis of phenolic metabolites formed in the organism, especially those that could come from microbiota metabolism, would help to understand these benefits. The aim of this study was to determine the widest urinary metabolomic fingerprinting of phenolics and microbial-derived phenolic acids (n = 61) after regular intake of DRW in men at high cardiovascular risk by UPLC-MS/MS using a targeted approach. Up to 49 metabolites, including phase II and microbial phenolic metabolites, increased after DRW consumption compared to baseline (P < 0.05). The highest percentage of increase was found for microbial metabolites from anthocyanin degradation such as syringic, p-coumaric, gallic acids and pyrogallol and from flavan-3-ols degradation such as hydroxyphenylvalerolactones and (epi)catechins. These findings provide the most complete metabolic fingerprinting after wine consumption, amplifying the spectrum of microbial derived metabolites and their potential bioactivity related with health benefits.