The homeostasis of micronutrients is of vital importance for all living organisms. We recently described an emerging role for flavonoids in metal homeostasis and tolerance in plants. Flavonoids are phenolic compounds with antioxidant properties which play a pivotal role in human health and diet, and are major actors during plant stress responses. Ionomic, transcriptomic and metabolomic data from Arabidopsis species showing contrasting metal tolerance and accumulation highlight a new role for flavonoids in the regulation of metal homeostasis and adaptation to extreme metallic environments. A major role for flavonoids during metal stresses was confirmed by using A. thaliana mutants impaired in flavonoid biosynthesis and signal transduction. Moreover, Nuclear Magnetic Resonance data also support flavonoids ability to form a complex with metals. However, no information is available on the role of flavonoids in the regulation of metal uptake, translocation and accumulation in plants. Our research aims at filling this gap by studying physiological, molecular and biochemical processes that plants use to regulate micronutrient homeostasis. We believe that a better understanding of flavonoids in the regulation of metal homeostasis can contribute to the enhancement of sustainable agriculture, food security and food quality, and to new tools in phytoremediation.