Pruning wood is usually crumbled and left on the soil surface or incorporated in vineyard soil and can represent an inoculum source for various pathogens, including wood pathogens. In the present work, the effect of in situ composting of pruning wood on both wood pathogens and the overall microbial composition was studied. The first experiment aimed to evaluate the effect of the high temperatures reached in the compost on the viability of some wood pathogens. Pieces of pruned wood collected from non-symptomatic plants were sterilized, inoculated with Phaeomoniella chlamydospora, Phaeoacremonium minimum, and Cadophora luteo-olivacea, incubated for a month at 25°C and exposed to a heat treatment at 60°C or left at 25° C. The heat treatment caused, after 5 days of exposure, the complete devitalisation of the pathogens. A second experiment aimed to compare traditional practices for pruning wood management with composting, evaluating their effect on the presence and viability of pathogenic populations and the microbial community in general. Composting significantly reduced both the quantity and viability of fungal species associated with wood diseases.