The continuum hypothesis states that both deterministic and stochastic processes contribute to the assembly of ecological communities. However, the contextual dependency of these processes remains an open question that imposes strong limitations on predictions of community responses to environmental change. We measured community and habitat turnover across multiple vertical soil horizons at 183 sites across Scotland for two microbial groups, both dominant and functionally vital components of all soils, that differ substantially in their growth habit and dispersal capability (bacteria and fungi). We found that habitat turnover was the primary driver of bacterial community turnover in general, although its importance decreased with increasing isolation and disturbance. Fungal communities, however, exhibited a highly stochastic assembly process, both neutral and non-neutral in nature, largely independent of disturbance. These findings suggest that increased focus on limitations to dispersal and biotic interactions within assemblages are necessary to manage and conserve the key ecosystem services provided by these assemblages.