Migrating diatoms are microscopic ecosystem engineering organisms that have functional consequences on the seascape scale by significantly contributing to the microphytobenthos biofilm. The microphytobenthos biofilm is a thin photosynthesising layer that covers the sediment on intertidal flats. It fuels the food web, increases sediment stability, and enhances the deposition of particles, providing ecosystem services to coastal communities. Here we tested the effect of another ecosystem engineering habitat, intertidal blue mussel reefs, on the composition and properties of migrating diatom communities. Small-scale reefs constructed in the intertidal mimicked and reinforced the natural pattern in diatom community composition and function that we documented in the field. The field experiment adding small reefs to the intertidal ran from 30 April to 10 June 2015 and the field samples were collected around a natural blue mussel bed on the same tidal flat on 7 October 2015 (N 53.489 degrees, E 6.230 degrees). Both the constructed small-scale reefs and the natural reef changed the community composition of diatoms in the biofilm by promoting higher numbers of smaller-sized cells and species. Small diatoms have higher growth and gross photosynthesis rates, indicating that this explains the higher production and chlorophyll-a concentration of the biofilm measured on natural intertidal shellfish reefs. Our results showed that shellfish reefs have a large impact on biofilm functioning. However, biofilms are also fuel for the shellfish, indicating that the two very different ecosystem engineers may facilitate coexistence on tidal flats through a positive feedback loop.