Despite the importance of trace metal availability for plant life, the complex intracellular mechanisms to regulate trace metal homeostasis are still poorly understood to date. Such regulatory networks have to comprise the sensing, storage and detoxification of metals as well as the incorporation of metal and metal containing cofactors into proteins. The complement of metal binding proteins and metal containing protein complexes within these networks as well as proteins that do not bind a metal but that possess metal-dependent expression dynamics represent the metalloproteome of a cell. To determine the dynamics and individual key players of such a complex system, proteomics as a whole systems approach reflects an appropriate strategy to progress in this subject. In this review we focus on recent advances in deciphering the complex regulatory networks of iron and cadmium homeostasis in plants by employing proteomics approaches. Hereby, iron is used as an example to describe the adaptation to trace metal deficiency whereas the complex adaptational strategies towards metal toxicity are exemplified for the non-essential toxic metal cadmium.