Background Cytoscape is an open-source software to visualize and analyze networks. However, large networks, such as protein interaction networks, are still difficult to analyze as a whole. Methods Here, we propose Clust&See3.0, a novel version of a Cytoscape app that has been developed to identify, visualize and manipulate network clusters and modules. It is now enriched with functionalities allowing custom annotations of nodes and computation of their statistical enrichments. Results As the wealth of multi-omics data is growing, such functionalities are highly valuable for a better understanding of biological module composition, as illustrated by the presented use case. Conclusions In summary, the originality of Clust&See3.0 lies in providing users with a complete tool for network clusters analyses: from cluster identification, visualization, node and cluster annotations to annotation statistical analyses.