One of the greatest challenges in heritage management is to find a balance between the demands of visitor access and heritage conservation. The income generated prevents decay and benefits the conservation of buildings. At the same time, cultural tourism can accelerate the deterioration of buildings from increased use and an increase in agents harmful to conservation. This unique research analyses the influence of building use at San Juan del Hospital, the oldest church in the city of Valencia. Its architectural characteristics and the climate of the city mean that visits to the building put the conservation of its heritage assets at risk. Monitoring data from the summer months were put into a digital twin generated from a heritage building information model (HBIM), and the modelling of visitor numbers and the impact on indoor environmental quality was conducted. Monitoring and simulations confirmed that visitor numbers need to be reduced or mechanical conditioning systems need to be installed to prevent damage to the heritage artefacts within the building. This research provides building managers with information to make informed decisions about the preventive maintenance of heritage buildings. This research also demonstrates for the first time the value of using monitoring and a digital twin for conservation management.