Grapevine trunk diseases (GTDs) are caused by cryptic complexes of fungal pathogens andhave become a growing problem for new grapevine (Vitis vinifera) plantations. We studied the roleof the nursery, variety, and rootstock in the composition of the fungal communities in root collarsand graft unions of planting material in Catalonia (NE Spain). We compared necrosis and fungalcommunities in graft unions and root collars at harvest, and then after three months of cold storage.We evaluated combinations of eleven red and five white varieties with four common rootstockscoming from six nurseries. Fungal communities were characterized by isolation and metabarcodingof the ITS2 region. Our data suggests that nursery followed by rootstock and variety had significanteffects on necrosis and fungal community structure in graft and root tissues. Within the plant, wefound large differences in terms fungal community distribution between graft and root tissues. Graftunions housed a significantly higher relative abundance of GTD-related Operational Taxonomic Units(OTUs) than root collars. More severe necrosis was correlated with a lower relative abundance ofGTD-related OTUs based on isolation and metabarcoding analyses. Our results suggest that nurseriesand therefore their plant production practices play a major role in determining the fungal and GTD-related fungal community in grapevine plants sold for planting. GTD variation across rootstocks andvarieties could be explored as a venue for minimizing pathogen load in young plantations.