Castanea sativa is a high-value tree species whose stands have faced significant threats over the past century. The occurrence of one such threat, Chestnut Red Stain—a heartwood discoloration caused by the fungus Fistulina hepatica—has recently increased. This disease devalues the timber by up to 70% due to the rejection of stained wood by the industry. This study aimed to evaluate the effects of three management strategies on the occurrence of F. hepatica in chestnut coppice stands. Additionally, the co-occurrence of F. hepatica and Cryphonectria parasitica, both highly prevalent in the study area, was assessed. In 2013, three different silvicultural treatments were applied to five plots. Seven years later, the stand characteristics were measured, and the incidence of F. hepatica was evaluated using molecular tools. Data modeling revealed that the quadratic mean diameter before the interventions was related to the incidence of F. hepatica. Our results suggest that the thinning at earlier stand stages may be more critical than the type or intensity of the thinning in reducing the incidence of the fungus in the mid-term. This finding provides forest managers with new guidance to improve silvicultural treatments and prevent F. hepatica damage.