The aim of the present study was to examine the short- and long-term effects of changes in vegetation structure caused by shrub removal and mowing on isopod diversity and composition in Natura 2000 habitats of Mátra Landscape Protection Area. Species richness and isopod diversity increased in the short term as a result of annual changes in vegetation; however, the values of both indices were reduced in the long term. The changes in vegetation structure on a regional scale led to a reduced isopod diversity in the short and long term. The changes in vegetation structure caused alterations in community structure in the long term. We conclude that changes of vegetation structure have a negative effect on species richness and the diversity of isopod communities in the long term.