AbstractMesophotic coral ecosystems (MCEs) have historically been considered more stable than shallow reefs and thus suggested to provide refuge to coral reef communities against natural and anthropogenic impacts. Despite this assumption, a growing body of literature has shown that deep reefs are not immune to natural disturbance. Here, based on our in situ observations, we propose that disturbance may actually represent an important mechanism for maintaining biodiversity in MCEs, as is the case for shallow reefs. Our observations suggest that disturbances can provide microhabitat and space necessary for the recruitment and occurrence of different species, increasing overall diversity. Since bioerosion rates are lower at depth, and most well‐developed coral reefs on MCEs are formed by dense aggregations of a single or a few species, intermediate levels of disturbance could represent a critical driver of community structure balancing. Therefore, instead of long‐term stability, intermediate disturbances should be expected on MCEs. However, high frequency and intensity of natural disturbances, or their association with anthropogenic stressors, might have stronger negative impacts on MCEs than on shallower reefs due to slower coral growth and calcification rates.