Protein-protein interaction networks (PPIN) enable the study of cellular processes in organisms. Visualizing PPINs in extended reality (XR), including virtual reality (VR) and mixed reality (MR), is crucial for exploring subnetworks, evaluating protein positions, and collaboratively analyzing and discussing on networks with the help of recent technological advancements. Here, we present BioNet-XR, a 3D visualization framework, to visualize PPINs in VR and MR environments. BioNet-XR was developed with the Unity3D game engine. Our framework provides state-of-the-art methods and visualization features including teleportation between nodes, general and first-person view to explore the network, subnetwork construction via PageRank, Steiner tree, and all-pair shortest path algorithms for a given set of initial nodes. We used usability tests to gather feedback from both specialists (bioinformaticians) and generalists (multidisciplinary groups), addressing the need for usability evaluations of visualization tools. In the MR version of BioNet-XR, users can seamlessly transition to real-world environments and interact with protein interaction networks. BioNet-XR is highly modular and adaptable for visualization of other biological networks, such as metabolic and regulatory networks, and extension with additional network methods.