Soil microbial communities regulate the fate of soil organic matter and allow plants to adjust to external conditions, tolerate stresses and modulate their nutrition in forest ecosystems. Yet, the long-lasting effects of different forest harvesting intensities on soil microbial communities remain poorly understood. We assessed even-aged (clear-cuts) and uneven-aged (partial harvests; 30% by single-tree selection) management effects on bacterial and fungal abundance and fungal community composition in the forest floor 5, 15 and 30 years after harvesting, relative to unmanaged old-growth controls, in a shade-tolerant hardwood forest in southern Quebec, Canada. Bacteria abundance in even-aged managed forests was significantly higher than in unmanaged forests over both the short- and long-term. Five years after harvesting, fungal species richness in even-aged (331 OTU) and uneven-aged (323 OTU) managed forests was significantly lower than in unmanaged forests (380 OTU). At the same time, fungal community dissimilarity and the proportion of fungal pathogens and parasites in even-aged managed forests were significantly higher than in unmanaged forests. The significant differences in fungal community composition between unmanaged forests and managed forests observed in the short-term (5 years after harvesting) become negligible in the long-term (30 years after harvesting). No significant effect of forest harvesting treatments on the proportion of saprotrophic fungi or fungal phylogenetic diversity was observed. Uneven-aged managed forests and unmanaged forests were associated with higher concentrations of P and C in the forest floor, higher forest density and diversity, and higher proportions of symbiotic fungi. •Forest harvesting altered soil fungal communities, especially over the shorter-term.•Forest harvesting altered more importantly bacteria than fungi in the forest floor.•Long-undisturbed forests were associated with higher proportions of symbiotic fungi.