Traditional clear-fell forestry greatly alters community structure and ecosystem function within boreal forests and alternative management practices may reduce these impacts. Continuous-cover forestry can maintain similar invertebrate and plant communities to unmanaged forest, but whether this extends to soil fungal communities remains unclear. Within four sites across the mid-boreal zone of Sweden, we conducted a comprehensive study to assess the impact of continuous-cover and clear-felling on soil fungi and chemical properties within Norway spruce dominated forests, using unmanaged forest as a control. We sampled soils for chemical properties (pH, carbon, nitrogen, C/N and Organic matter) and used both surveys of fungal fruiting bodies and state of the DNA metabarcoding techniques to assess treatment effects on soil fungal communities. We found that forest management practices had significant effects soil pH, C and C/N ratio and that continuous-cover forestry had more similar soil properties to unmanaged forest. Furthermore, the biodiversity of fruiting bodies, as expressed by species richness and Shannon’s diversity index, was higher in continuous-cover forestry and unmanaged forest compared to clear-felled areas. However, the opposite was true for the diversity of soil fungal communities, which was probably due to the high level of disturbance in clear-felled areas, and thus, ample habitat for early successional colonisers and some remnants of mature forest communities. However, in agreement with predictions we found that the composition of both fruiting body and soil fungal communities broadly similar in continuous-cover and unmanaged forest, but fundamentally different to clear-felled areas. Consequently, our findings highlight that continuous-cover forestry is an alternative to conventional practise, maintaining communities associated with unmanaged forest and mimicking natural disturbance regimes.