The phylogeography of many forest-dwelling species in Europe is well understood. However, our knowledge regarding the genetics of saproxylic beetles remains insufficient. This knowledge gap extends to understanding the influence of both quaternary history and contemporary forest dynamics on population genetics. To fill this gap, we conducted a systematic review and meta-analysis of recent literature concerning saproxylic beetle taxa with available genetic data. We include both threatened and common species in our study, which enabled us to generalize our findings to the whole saproxylic community. Results suggest a latitudinal decrease in diversity in most species, likely influenced by Pleistocene glaciation and subsequent population expansions from southern refugia. Additionally, we observed an east–west gradient in diversity, with threatened species exhibiting higher diversity towards the east. This may reflect historical forest dynamics and anthropogenic pressures, such as heavy wood logging in Western Europe. Similarly, we found a pattern along altitude, with populations in higher elevation forests, which are often more natural, exhibiting higher diversity. Furthermore, we identified distinct phylogenetic units or genetic clusters in southern Europe reflecting the distribution of glacial refugia. For some taxa, distinct units were also reported in eastern Europe where populations spread from Asian refugia. Central Europe showed a high number of phylogenetic units, although unique (private) clades or clusters were absent. Most likely it is an effect of the presence of beetles that originated from various refugia belonging to different phylogenetic units.This study brings insights into general phylogeographic patterns, which have previously been examined only for single representatives of saproxylic beetles. It should also help in the proper planning of conservation and management efforts for wood-dwelling beetles.