<p>Ectomycorrhizal fungi represent a key component of forest ecosystems, contributing significantly to tree nutrition, stress tolerance, and overall ecosystem resilience. In the Mediterranean region, cork oak (<i>Quercus suber</i> L.) forests, have significant ecological and economic value, and their vitality strongly depends on these belowground mutualistic relationships. Although previous studies have investigated the diversity and function of ectomycorrhizal fungi, several aspects concerning their ecological dynamics remain inadequately understood, particularly in cork oak forests. This study investigates the structural and dynamics of ectomycorrhizal fungal communities in cork oak forests of Sardinia located on granitic, basaltic, and trachytic substrates and subjected to different management practices (natural, grazed, and ploughed). We assess how forest management and seasonal variability interact with lithological conditions to shape community structure and diversity. Three cork oak stands for each lithological substrate (nine in total) were selected in areas where all the three forestry managements were present. Two transects were established in each stand, and soil samples were collected during spring and autumn to assess seasonal variations in the ectomycorrhizal community. In total, 82,345 ectomycorrhizal root tips were morphologically characterized and classified in 167 morphotypes based on morpho-anatomical characteristics. From these, 120 were successfully assigned to distinct Operational Taxonomic Units (OTUs) through internal transcribed spacer (ITS) barcoding. Our results indicate that lithological substrate, management system, and sampling season significantly influence the structure and composition of ectomycorrhizal communities. Notably, ploughing caused a marked reduction in fungal richness, highlighting the sensitivity of these communities to soil disturbance.</p>