A study was carried out on biodeterioration processes at six Jewish cemeteries in north-eastern Italy, which were generally subject to very poor maintenance. Several crustose lichens, as well as ruderal wooden plants, were found growing differentially on stone types in the various cemeteries. Lichens colonizing gravestones and woody plants were examined through field observations and several microscopic analyses. Evaluations were carried out on selected species and some damage risk indices were applied. The Index of Lichen Potential Biodeteriogenic Activity (LPBA) was calculated for Nanto stone, which suffered the highest degree of deterioration. The Hazard Index (HI), which is independent from the lithotype, was calculated for all the wooden plants. We also analyzed the ecological relationships of such colonization in order to evaluate indirect conservation treatments. The various lichen species were causing differential interactions with the stone, sometimes contributing in cracking and detachment of fragments. Their potential aggressiveness is mainly attributable to the different lithotypes, but also to changes in maintenance, tree canopy cover, and eutrophication. We have made suggestions for an appropriate plant management that considers their environmental, ornamental and symbolic importance in such context. For the stone conservative treatments against lichens, we also carried out tests on selected biocides.