Incorporating healthcare data from different sources is crucial for a better understanding of patient (sub)populations. However, data centralization raises concerns about data privacy and governance. In this work, we present an improved infrastructure that allows privacy-preserving analysis of patient data: vantage6 v3. For this new version, we describe its architecture and upgraded functionality, which allows algorithms running at each party to communicate with one another through a virtual private network (while still being isolated from the public internet to reduce the risk of data leakage). This allows the execution of different types of algorithms (e.g., multi-party computation) that were practically infeasible before, as showcased by the included examples. The (continuous) development of this type of infrastructure is fundamental to meet the current and future demands of healthcare research with a strong emphasis on preserving the privacy of sensitive patient data.