Abstract Forest dynamics are driven by micro‐disturbances leading to gap formation. Root rot pathogens can cause mortality to adult trees, which die forming gaps. However, little is known about the biotic and abiotic factors that govern gap creation and expansion such as tree infection or drought resilience, and what are the consequences for nutrient cycling and soil microbiota. We studied the dynamics of gaps created by Heterobasidion abietinum in mountain silver fir (Abies alba) forests from the Spanish Central Pyrenees. Tree‐ring width information was used to evaluate growth patterns of trees located within and at the edge of gaps and under closed canopy conditions. We analysed soil nutrient content and microbial structure at different positions with respect to the gap. Soil fungal community was also characterized by sequencing the ITS2 region. Gaps created by H. abietinum ranged 582–1072 m2 and gathered large amounts of standing and laying dead wood biomass amounting to up to 500 m3 ha−1 of coarse woody debris. This indicates that tree mortality had been occurring over decades, and it was preceded by a long‐term growth decline and impaired drought resilience. Root rot affected trees beyond the current limit of the gaps leading to growth decline, preventing canopy closure and allowing the release of suppressed trees within the gap. Gap formation did neither affect soil fertility nor fungal and bacterial biomass and diversity, but long‐distance ectomycorrhizal fungi were more abundant within gaps. Synthesis. Root rot pathogens play key ecological roles in forest dynamics at fine spatial scale. Heterobasidion abietinum infection, and its interaction with drought, creates and expands gaps by killing large trees and preventing surrounding trees from closing the gap. The survival of mycorrhizal networks to gap formation suggests little disruption of soil fungal communities.