In this work a method is proposed to estimate the effect of indoor microclimate on the risk of degradation of ancient materials stored in historical buildings. The method, which combines microclimate observations and dynamic simulation, has shown to be strategic in preventive conservation of historical buildings. Indeed, once the building model is calibrated, it can be effectively used for evaluating the microclimate control solutions on the conservation reducing general degradation risks. The method has been applied to a historical building close to Rome, where deteriorations in ceilings occurred and visitors complain about thermal discomfort. First, the HVAC system in the model has set in order to guarantee both thermal comfort and adequate condition for the conservation of the material. Then, the crack width of wooden ceiling has been estimated by means of an empirical model based on indoor temperature and relative humidity data and validated with the measurements of the crack width. It was found a reduction of annual variation from 0.4 mm to 0.2 mm, experimented by panels, and an improvement of maximum daily variation, especially in winter and summer (less than 0.01 mm on average).