Metalloproteins play major roles in cell metabolism and signalling pathways. In many cases, they show moonlighting behaviour, acting in different processes, depending on the physiological state of the cell. To understand these multitasking proteins, we need to discover the partners with which they carry out such novel functions. Although many technological and methodological tools have recently been reported for the detection of protein interactions, specific approaches to studying the interactions involving metalloproteins are not yet well developed. The task is even more challenging for metalloproteins, because they often form short-lived complexes that are difficult to detect. In this review, we gather the different proteomic techniques and biointeractomic tools reported in the literature. All of them have shown their applicability to the study of transient and weak protein-protein interactions, and are therefore suitable for metalloprotein interactions. Metalloproteins play major roles in cell metabolism and signaling pathways, showing a moonlighting behaviour, which depends on the physiological state of the cell. Understanding these multitasking proteins compels us to discover their partners with which to carry out such novel functions. We gather the different proteomic techniques and biointeractomic tools, whose applicability to the study of transient protein-protein interactions make them suitable for metalloprotein interactions.