Marine inputs from seabirds (in the form of guano) to terrestrial coastal communities play an important role in supporting aboveground food webs. However, little is known about the importance of seabird-derived nutrient inputs for belowground food webs and their function relative to other factors that regulate belowground communities. Here, we tested the relative importance of nutrient enrichment from seabirds and grazing, a known driver of belowground properties, in determining the structure and function of the soil food web in an island system. This was tested by measuring the size and composition of the microbial community, the abundance of nematode feeding groups and rates of decomposition and net nitrogen (N) mineralisation in soil samples collected from grazed and ungrazed plots at coastal and inland locations, representing sites of high and low seabird influence respectively, on the Isle of May in the Firth of Forth, east Scotland. We found that proximity to seabird breeding colonies, and associated greater input of seabird-derived N, stimulated the size of the soil microbial biomass and the abundance of bacteria relative to fungi in the soil microbial community relative to inland areas that received significantly less N. Despite this, proximity to seabird colonies had no detectable effect on rates of decomposition or N-mineralisation. The short-term removal of mammalian grazers, in the form of rabbits, had only limited effects on the structure of the soil food web, mainly affecting the abundance of bactivorous nematodes which were greater in grazed than ungrazed situations. However, cessation of grazing did impact significantly on rates of N-mineralisation and decomposition, which were higher and lower in grazed than ungrazed situations respectively. In conclusion, our study provides evidence that allochthonous nutrient inputs from seabirds have significant impacts on the composition of the soil microbial community, and that these effects outweigh short-term effects of grazers as a driver of soil food web structure in the island system studied. Overall, our results indicate the important roles that natural sources of N and grazing play as drivers of soil food webs and their function. © 2009 Elsevier Ltd. All rights reserved.