Sacred forests are an integral component of the mountainous cultural landscape of northern Greece, hypothesized to be the result of both ecological processes and site-specific forest management regimes through strict religious prohibition. These practices acted as constraints on natural forest development by suppressing understorey growth, while prohibition of woodcutting has preserved large trees. The aim of this study was to investigate the relative effects of physical site environment and management regimes on the structure and composition of woody plant groups in six such forests. Species rank-abundance curves, dissimilarity indices and cluster analyses were used to assess variation within and amongst the woody plant groups of the sites. Species abundance was found to be highly variable amongst the sites, with notable variation between canopy and understorey layers indicating dynamic change in floristics and structure. Cluster analysis revealed four main woody plant groups statistically associated with environmental variables (aspect) and forest management (different forest prohibition regimes, and presence/absence of infrastructure). Our results indicate that tree composition in sacred forests is associated with variation in environmental variables as well as with prohibition regimes. Exploring further the role of traditional management systems in shaping sacred forests structure is a relevant research path for designing effective conservation practices tailored to sacred natural sites facing cultural abandonment.