The paper presents the setpoint control for air heating in a church to minimize moisture related mechanical stress in wooden interior parts, with the focus on the preservation of a monumental organ. The setpoint operation of the heating, ventilation, and air conditioning (HVAC) system is evaluated by simulation using MatLab, COMSOL and Simulink models. The main model components are presented and combined in a single integrated Simulink model: (1) a HAMBase Simulink building model for simulating the indoor temperature and relative humidity, (2) a COMSOL partial differential equation model for simulating detailed dynamic moisture transport and related mechanical stresses in the monumental wood (organ) and (3) a Simulink controller model. The main advantage of the integrated model is that it directly simulates the impact of HVAC control setpoint strategies on the indoor climate and the related mechanical stresses in wooden objects, like a monumental organ. As control strategy the limited indoor air temperature changing rate is discussed. Recommendations from international literature suggest that a limitation of the relative humidity changing rate of 2 to 5RH%/h will preserve the interior of churches. This study shows that a limitation of indoor air relative humidity changing rate of 2RH%/h can reduce mechanical stresses by a factor of 2.5, compared to maximum capacity heating.