The consumption of low-alcohol fermented beverages has been related to cardiovascular health improvements. Although the underlying mechanism is not completely understood, (poly)phenols have been proposed as one of the mediators. The objective of this study was to evaluate the impact of a controlled intervention with beer on (poly)phenols metabolism in individuals with and without metabolic syndrome (MetS). 20 participants (MetS and control) who consumed a standardized amount of beer during 6 weeks were recruited. Phenolic compounds were assessed in urine. Different changes in phenolic compounds associated with chronic beer consumption were found, particularly related to hesperetin conjugates and to the degradation of phenolic compounds derived from flavonoids and lignans. Noteworthily, MetS and control participants differed in baseline urine phenolic compound profiles and in their metabolization. Significant differences were found in the production and excretion of key (poly)phenols-derived metabolites, such as increased naringenin phase II conjugates in healthy subjects, or increased bacterial flavonoid catabolites. Certain relationships were observed between the phenolic compounds with metabolic and anthropometric variables. These findings suggest that beer-derived (poly)phenols are differentially metabolized according to metabolic-health status, and that they may contribute to certain metabolic health benefits through the modulation of specific metabolic pathways.