Climate change is expected to have a severe impact on cultural heritage in the future. This study presents the methodology developed during the FP7 project Climate for Culture, of assessing the climate change impact on collection objects in cultural heritage buildings. The main innovation lies in coupling new high resolution future climate projections with building simulation tools in order to predict future indoor climate and identify future risks in historic buildings. The case study is an intermittently heated wooden chapel in Croatia. The whole building simulation model of the chapel was validated using a newly developed method of accuracy assessment in the context of preventive conservation. Even though modeling intermittent heating induces limitations in the model, it can be used for computing of future indoor data. Future indoor climate data was assessed for possible risks of biological, mechanical, and chemical damage to painted wooden panels using the newly developed specific climate risk assessment. When using this method of damage assessment on buildings with active climate control, especially with intermittent heating, it is recommended to determine the relevant season for the damage process in order to objectively analyze results.