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By influencing soil biota and nutrient cycling, plants can alter their fitness and that of their neighbours through plant-soil feedbacks. However, we need more detailed understanding of the biological causes of such feedbacks. This includes identifying the soil microbial guilds causing them. As most plant-soil feedbacks have been reported to be negative, the dominant paradigm is focused on the accumulation of soil pathogens. This neglects the full range of soil microorganisms likely to influence plant performance. Here, we studied plant growth responses to field-collected soil inocula in a large-scale greenhouse study coupled with next-generation sequencing. Although we found a high prevalence of negative plant-soil feedbacks, the microorganisms driving the responses were largely saprotrophs and N-cycling prokaryotes, not pathogens. These results show that negative plant-soil feedbacks need not be caused by trophic interactions, highlighting the need to bring back nutrient cycling as a central component of plant-soil feedbacks.