Changes in light/dark cycles and obesogenic diets are related to the disruption of circadian rhythms and metabolic disorders. Grape seed flavanols have shown beneficial effects on metabolic diseases and, recently, a circadian system modulation has been suggested to mediate their health-enhancing properties. Therefore, the aim of this study was to evaluate the grape seed (poly)phenol extract (GSPE) effects in healthy and obese rats after a light/dark cycle disruption. Forty-eight rats were fed a standard (STD) or cafeteria (CAF) diet for 6 weeks under STD conditions of a light/dark cycle (12 h light per day, L12). Then, animals were switched to a long (18 h light per day, L18) or short (6 h light per day, L6) photoperiod and administered a vehicle (VH) or GSPE (25 mg kg-1) for 1 week. The results showed changes in serum lipids and insulin and metabolomic profiles dependent on the photoperiod and animal health status. GSPE administration improved serum parameters and increased the Nampt gene expression in CAF rats and modified the metabolomic profile in a photoperiod-dependent manner. Metabolic effects of light/dark disturbance depend on the health status of the rats, with diet-induced CAF-induced obese rats being more affected. Grape seed flavanols improve the metabolic status in a photoperiod-dependent manner and their effects on the circadian system suggest that part of their metabolic effects could be mediated by their action on biological rhythms.