A transition to sustainable agricultural management may have large implications for soil biodiversity and functioning. Here, we sequenced bacterial, archaeal, and fungal communities in paired organic and conventional fields on marine clay and sand using a chronosequence that covered 25 years of conversion to organic management. We found that fungal diversity increased and community composition changed with time since conversion in organic, but also in paired conventional fields. Yet, shifts in microbial diversity and community composition were related to soil abiotic conditions, such as soil organic matter content. We conclude that environmental conditions play a more important role driving microbial community composition than time since conversion to organic management.