Background: The influence of farming on plant, animal and microbial biodiversity has been carefully studied and much debated. Here, we compare an isolate-based study of 196 Rhizobium strains to amplicon-based MAUI-seq analysis of rhizobia from 17,000 white clover root nodules. We use these data to investigate the influence of soil properties, geographic distance, and field management on Rhizobium nodule populations. Results: Overall, there was good agreement between the two approaches and the precise allele frequency estimates from the large-scale MAUI-seq amplicon data allowed detailed comparisons of rhizobium populations between individual plots and fields. A few specific chromosomal core-gene alleles were significantly correlated with soil clay content, and core-gene allele profiles became increasingly distinct with geographic distance. Field management was associated with striking differences in Rhizobium diversity, where organic fields showed significantly higher diversity levels than conventionally managed trials. Conclusions: Our results indicate that MAUI-seq is suitable and robust for assessing nodule Rhizobium diversity. We further observe possible profound effects of field management on microbial diversity, which could impact plant health and productivity and warrant further investigation.