Human activities can highly impact species that rely on man-made structures for shelter or nesting, and building modifications for pest control or maintenance can have hidden ecological consequences. The breeding of the western barn owl (Tyto alba; hereafter barn owl) is especially associated with agricultural and church buildings. It is well known that the renovation of churches and their architectural protection against unwanted animals have significantly reduced the availability of barn owl nesting sites in recent decades. However, other potential direct consequences of church modifications have not been investigated sufficiently. We demonstrated how improperly modified church towers can act as traps, allowing the owls to enter the building but preventing them from leaving, which can lead to mass mortality, as we documented in two cases. This study highlights the need for deeper and more multifaceted investigations of building protection in light of such consequences that have been generally hidden until now in order to protect the barn owl more effectively.