Phosphatases play an essential role in the regulation of protein phosphorylation. Less abundant than kinases, many phosphatases are components of one or more macromolecular complexes with different substrate specificities and specific functionalities. The expert scientific curation of phosphatase complexes for the UniProt and Complex Portal databases supports the whole scientific community by collating and organising small‐ and large‐scale experimental data from the scientific literature into context‐specific central resources, where the data can be freely accessed and used to further academic and translational research. In this review, we discuss how the diverse biological functions of phosphatase complexes are presented in UniProt and the Complex Portal, and how understanding the biological significance of phosphatase complexes in Caenorhabditis elegans offers insight into the mechanisms of substrate diversity in a variety of cellular and molecular processes. The UniProt Knowledgebase (UniProtKB) and Complex Portal databases facilitate the understanding of how protein phosphorylation is regulated by providing structural and functional information on phosphatase‐containing macromolecular complexes across a wide range of species. Using the Caenorhabditis elegans model organism as a basis, this review addresses the challenges in annotating protein complex data and summarises how the two databases differ in their approach to presenting phosphatase‐containing complexes.