Melatonin is an endogenous antioxidant hormone, which reduces with ageing and the low levels are associated with some chronic diseases. Germination of legumes increases the plant levels of melatonin, making sprouts a suitable food source of this hormone. However, information on its bioavailability after consumption is lacking. We aimed to evaluate in rats the effect of kidney bean sprout intake on the plasma levels of melatonin and metabolically related compounds (serotonin, 6-sulfatoxymelatonin), total phenolic compounds and total antioxidant capacity. In addition, we compared the plasma bioavailability derived from kidney bean sprouts versus synthetic melatonin intake. Kidney beans were germinated for 6 days and an extract was prepared in water. Male young Sprague Dawley rats were used; blood and urine samples were obtained before and after 90 min of administration of kidney bean sprout extract via a gavage. The plasmatic melatonin levels increased after sprout ingestion (16%, p < 0.05). This increment correlated with the urinary 6-sulfatoxymelatonin content, the principal biomarker of plasmatic melatonin levels (p < 0.01). Nevertheless, the phenolic compounds and antioxidant capacity levels did not exhibit any significant variation. The comparison of the bioavailability between the melatonin contained in the kidney bean sprouts and in a synthetic solution evidenced slightly higher levels of plasmatic melatonin (17%) in rats fed with the solution of synthetic melatonin. We conclude that kidney bean sprouts could be a good source of dietary melatonin and other bioactive compounds known to have health benefits.