Peatlands are under threat from land management, anthropogenic pollution and climate change. These factors are implicated in severe degradation of peatlands in the southern Pennines of northern England. Significant areas of unconsolidated bare peat are both highly vulnerable to peat erosion and resistant to natural re-vegetation. Restoration efforts during the last 30 years have included liming and fertilisation of bare peat allowing transient growth of introduced lowland grass species for peat stabilisation that facilitates establishment of Calluna vulgaris and other dwarf shrubs. Key restoration goals through re-vegetation of bare peat are to increase biodiversity, recover hydrological function, and retain carbon storage function. Below-ground bacterial and fungal communities were characterised in tandem across this vegetation mosaic using high-throughput sequencing of respective phylogenetic markers (16S and ITS1). Restoration activities were reflected in changes in plant cover and the below-ground microbial community, which may be of functional importance in relation to restoration goals and future land management planning. Ericoid mycorrhizal fungi and ectomycorrhizal taxa were highly represented whilst members of the Glomeromycota were present but rare. Microbial co-occurrence was observed through cross-kingdom network analysis of fungi and bacteria, identifying possible functional groupings of relevance to maintenance and restoration of peatland function.