Many ecological communities are enormously diverse. Variation in environmental conditions over time and space provides opportunities for temporal and spatial storage effects to operate, potentially promoting species coexistence and biodiversity. While several studies have provided empirical evidence supporting the significance of the temporal storage effect for coexistence, empirical tests of the role of the spatial storage effect are rare. In particular, we know little about how the spatial storage effect contributes to biodiversity over evolutionary timescales. Here, we report the first experimental study on the role of the spatial storage effect in the maintenance of biodiversity in evolving metacommunities, using the bacterium Pseudomonas fluorescens SBW25 as a laboratory model of adaptive radiation. We found that intercommunity spatial heterogeneity promoted phenotypic diversity of P. fluorescens in the presence of dispersal among local communities, by allowing the spatial storage effect to operate. Mechanistically, greater niche differences among P. fluorescens phenotypes arose in metacommunities with intercommunity spatial heterogeneity, facilitating negative frequency-dependent selection, and thus, the coexistence among P. fluorescens phenotypes. These results highlight the importance of the spatial storage effect for biodiversity over evolutionary timescales.