The growth conditions in different latitudes vary markedly with season, day length, light quality and temperature. Many plant species have adapted well to the distinct environments through different strategies, one of which is the production of additional secondary metabolites. Flavonoids are a widely spread group of plant secondary metabolites that are involved in many crucial functions of plants. Our understanding of the biosynthesis, occurrence and function of flavonoids has increased rapidly in recent decades. Numerous studies have been published on the influence of environmental factors on the biosynthesis of flavonoids. However, extensive long-term studies that examine the effect of the characteristics of northern climates on flavonoid biosynthesis are still scarce. This review focuses on the current knowledge about the effect of light intensity, photoperiod and temperature on the gene-environment interaction related to flavonoid biosynthesis in plants.