Populations trends of cave-dwelling bats in the Eastern Iberian Peninsula and the effect of placing a perimeter fencing around their roosts (to avoid human disturbance on breeding colonies) were evaluated from 1997 to 2014. The species with the highest relative abundance was Miniopterus schreibersii (62.4%), followed by Myotis myotis/blythii (18%), and both populations showed positive trends. On the other hand, Myotis capaccinii (6.2%), M. escalerai (4.8%) and M. emarginatus (0.9%) showed significant, but minor increases, particularly in recent years. Rhinolophus mehelyi (0.2%) displayed no significant trends, while a moderate population decline was recorded for R. euryale (5.1%). Rhinolophus ferrumequinum (2.2%) and R. hipposideros (0.1%) showed positive growth trends. The main assemblages in the evaluated roosts were formed by Myotis myotis/blythii, Miniopterus schreibersii and R. ferrumequinum. This denotes their less specific requirements or greater flexibility when selecting roosts, compared with other species, except for M. capaccinii and R. mehelyi. No significant differences were found between roosts with different levels of protection, but there were positive trends in the protected roosts. Most non-fenced cavities showed negative trends during the period evaluated. We did not rule out other factors, such as requiring habitats with optimum food sources next to maternal roosts, which could affect population growth. The selectivity of some species of bats for certain caves will be essential for the preparation of management plans for certain roosts. Four of the seven risk factors documented for European bats affect studied population. Myotis blythii, M. myotis and Rhinolophus euryale would be most affected by a reduction in the areas they currently occupy.