The specific interactions of anionic metal‐oxo clusters, known as polyoxometalates (POMs), with proteins can be leveraged for a wide range of analytical and biomedical applications. For example, POMs have been developed as selective catalysts that can induce protein modifications and have also been shown to facilitate protein crystallization, both of which are instrumental in the structural characterization of proteins. POMs can also be used for selective protein separation and enzyme inhibition, which makes them promising therapeutic agents. Hence, understanding POM‐protein interactions is essential for the development of POM‐based materials and their implementation in several fields. In this Review we summarize in detail the key insights that have been gained so far on POM‐protein interactions. Emphasis is also given to hybrid POMs functionalized with organic ligands to prompt further research in this direction owing to the promising recent results on tuning POM‐protein interactions through POM functionalization.