The COVID-19 pandemic has generated new needs due to the associated health risks and, more specifically, its rapid infection rate. Prevention measures to avoid contagions in indoor spaces, especially in office and public buildings (e.g., hospitals, public administration, educational centres, etc.), have led to the need for adequate ventilation to dilute the possible concentration of the virus. This article presents our contribution to this new challenge, namely the Ventilation Early Warning System (VEWS) which has aims to adapt the operation of the current Heating, Ventilating and Air Conditioning (HVAC) systems to the ventilation needs of diaphanous workspaces, based on a Smart Campus Digital Twin (SCDT) framework approach, while maintaining sustainability. Different technologies such as the Internet of Things (IoT), Building Information Modelling (BIM) and Artificial Intelligence (AI) algorithms are combined to collect and integrate monitoring data (historical records, real-time information, and location-related patterns) to carry out forecasting simulations in this digital twin. The generated outputs serve to assist facility managers in their building governance, considering the appropriate application of health measures to reduce the risk of coronavirus contagion in combination with sustainability criteria. The article also provides the results of the implementation of the VEWS in a university workspace as a case study. Its application has made it possible to detect and warn of inadequate ventilation situations for the daily flow of people in the different controlled zones.