Benthic diatoms are the dominant primary producers in intertidal mudflats and constitute a major source of organic carbon to consumers and decomposers residing within these ecosystems. They typically form biofilms, whose species richness, community composition and productivity vary in response to environmental drivers and self-organising processes. Here, we investigated whether bacteria could affect diatom community composition and vice versa, and how this influences the diversity-productivity relationship. Using axenic experimental communities with three common benthic diatoms, Cylindrotheca closterium, Navicula phyllepta and Seminavis robusta, we observed an elevation in algal biomass production in diatom cocultures in comparison to monocultures, largely mediated by complementarity effects. The presence of bacteria increased this effect, mainly by decreasing the productivity of the diatom monocultures but not the co-cultures. Furthermore, the effect of bacteria on diatom growth appeared to be species-specific, resulting in compositional shifts when different diatom species were grown together. The effect of the diatoms on the bacteria also proved to be specific as different diatoms developed different bacterial communities. Our data suggest that interactions between bacteria and diatoms are a key factor in structuring the benthic microbial community in mudflats and the functioning of the community.