Forest management aimed to maximize timber production might impact soil fungi, especially those symbiotically associated to tree roots. In this study, we analyse the temporal dynamics of soil fungi along five sampling years after tree removal in a managed Pinus sylvestris stand in northern Spain, where timber production is combined with regular mushroom harvesting. Two management methods were tested: total and partial clear-cutting leaving retention trees for seedling regeneration. Undisturbed, uncut plots were also included in the experiment as a control treatment. The whole fungal community (phylotypes and ecological guilds) were analysed by high-throughput Illumina MiSeq sequencing of fungal ITS1 amplicons. We hypothesized that (1) ectomycorrhizal fungal communities will decrease after both clear-cutting treatments with a concurrent increase in the abundance of saprotrophs, (2) the abundance and diversity of the ectomycorrhizal guild will be more preserved in partially clear-cut than in total clear-cut plots, and (3) the overall fungal diversity will decrease in the cut plots leading to major losses of ectomycorrhizal species. Our results show that soil fungal composition changed across the five years after clear-cutting by decreasing ectomycorrhizal fungi and increasing saprotrophs. However, these changes did not significantly affect fungal diversity and there were taxa-specific responses to tree harvest treatments.