Two clonal selections of lemon tree (Citrus limon Burm. f. cv. Fino), named Fino-49-5 and Fino-95, were studied to ascertain the influence of genetic (clone) and environmental (season) factors on the human-health bioactive compounds of lemon juice (vitamin C and flavonoids) and the possible relationship between composition and in vitro antioxidant capacity (2,2-diphenyl-1-picrylhydrazyl, 2,2'-azino-bis(3-ethyl-benzothiazoline-6-sulfonic acid), and ferric reducing antioxidant power) of the juice. The cultivar Fino-49-5 performed better in terms of flavonoid and vitamin C contents. Variability in the weather conditions determined, at least in part, differences in the content of lemon juice bioactives more importantly than the genetic background did. Therefore, the food industry would have phytochemically rich and nutritive lemons with practically complete independence of the harvest time and the selected cultivar.