Active management to encourage the expansion of native pine woodland onto neighbouring moorland has been suggested as a tool to promote increases in forest area to combat climate change. Low intensity burning has previously been shown to increase pine seedling establishment, however the effect of this on below-ground diversity and functioning in these important terrestrial carbon stores is equivocal. Here, we assessed the effect of a single burn and grazing exclosures after a 6 year period on soil microbial respiratory activity and fungal community structure using terminal restriction fragment polymorphism (T-RFLP) analysis. The combined data suggest that the strategy of a single prescribed burn to facilitate Scots pine establishment had no lasting effect on either fungal taxonomic richness, fungal community composition or microbial activity. Thus, our findings support the proposed use of single, low intensity, prescribed burns in regenerating Scots pine forests as a low impact management tool.