Microbial communities often thrive in spatially confined environments, such skin pores or intestinal crypts. These microhabitats foster stable populations that contribute to the diversity and functionality of microbiomes. However, the impact of spatial constraints on microbial community assembly and evolution remains poorly understood. By monitoring and modeling microbial populations under controlled microfluidic confinement, we uncover a rich spectrum of dynamical patterns that are controlled by the competition between density-dependent outflow and population growth. Our findings reveal that passive diffusion, regulated by population density, can push a reproducing community to a jamming threshold—leading to a complete loss of mixing and intra-species competition. The emerging sensitivity to scale may be viewed as a rigorously quantifiable in vitro version of similar effects reported in the field of island biogeography, and underscores the need to control for scale in microbial ecology experiments. Systematic, flow-adjustable length scale variations may serve as a promising strategy to elucidate further scale-dependent tipping points and to rationally modulate the stability and resilience of microbial colonizers.