Agricultural intensification has been vital for meeting global food demand but has caused environmental degradation. This has disrupted the ability of soil to provide vital ecosystem services. Organic farming is often thought to conserve and utilise soil ecosystem services, and thus be a more sustainable method of food production than conventional farming. However, evidence for this is equivocal, and little is known of the potential trade-offs between soil functions, which can be classified as supporting and provisioning ecosystem services, in conventional and organic systems. In addition, few studies have simultaneously examined how surrounding landscape heterogeneity affects soil functions in agriculture. In this study we investigated the effects of farming method (conventional versus organic) and landscape heterogeneity (100 m, 500 m and 1000 m radius) on indicators of soil ecosystem services: soil organic carbon (SOC), total nitrogen (TN), water holding capacity (WHC) and plant-available phosphorous (P) (measures of carbon storage and nutrient retention); net N mineralisation and microbial community composition and biomass (nutrient cycling); and crop yield. We found no effect of landscape heterogeneity, and no differences in any of the measured soil and microbial variables between conventional and organic farms, apart from net N mineralisation, which was higher in organic farms. However, conventional farms had significantly greater yield than organic farms, and there was no apparent trade-off between increasing yield and the level of supporting ecosystem services. The organic farms in this study appear to have been intensively managed, with a straight substitution of organic inputs for chemicals, but little other effort to enhance soil fertility. For example, the organic farms applied large quantities of manure compared with conventional farms but conducted mechanical weeding (harrowing), whereas conventional farms applied herbicides. This repeated soil disturbance may cause rapid organic matter mineralisation and undermine the ability of these organic farms to retain carbon and nitrogen. The terms ‘organic’ and ‘conventional’ agriculture both cover a wide variety of farming methods, some of which enhance or deplete ecosystem services more than others. To develop truly sustainable methods of agriculture, research should focus on the effects of specific farming practices, rather than the labels ‘conventional’ and ‘organic’.