Digital Twins (DTs) are becoming an empowering and pivotal element in many industries to exploit modern IT technologies across all sectors and gain significant benefits from preexisting as well as greenfield systems. This paper introduces a novel approach to building management and research in laboratory environments, utilizing Building Information Modeling (BIM), DTs, the Internet of Things (IoT), and Extended Reality (XR). The work focuses on generating accurate 3D building models from point cloud scans, improving BIM’s utility in structures lacking pre-existing digital models. Central to this approach is the integration of IoT sensors, tracking indoor air quality and occupancy. This data, combined with DTs of laboratory equipment, facilitates dynamic insights of transdisciplinary work at research and educational projects. Our models uniquely provide live data interaction, seamlessly linking the virtual and physical realms through DTs and XR technologies as an immersive interface. One of the problems at research institutes is the broad range of hazardous measuring devices, some of which require urgent safety precautions. Therefore, based on our models and technologies, we propose an XR-based collaborative platform for transdisciplinary research teams enabling immersive and intuitive interaction. By comprehensively gathering all the data, it is possible to continue investigating how social dynamics affect research environments and projects. This approach aims to make technology more attuned to the social dimensions of laboratory use. The paper highlights the potential of BIM, DTs, IoT, and XR to not only create and update models post-construction but also to enrich them with operational data, offering a socially aware perspective in research management.