Stream sediments move at low flow forming migrating ripples. These ripples can cover substantial areas where benthic communities experience erosion-resting cycles of sand grains. Sediment surface and interstitial space is colonized by meiobenthos, an assemblage of microscopic invertebrates. Here we describe how sediment migration influences the structure of the meiobenthic community. We sampled migrating and stationary sediment patches in five streams. Sediments in migrating ripple patches were characterized by coarser grain size and higher oxygen concentration, but less organic matter and chlorophyll than stationary patches. Meiobenthos was more abundant in the superficial layer of stationary sediment compared to the underlying layer, whereas comparable abundances were observed in both layers of migrating patches. This suggests that ripple migration enhances the vertical mixing of interstitial communities. Among the environmental drivers measured, meiobenthos community structure was most related to sediment transport regime: Rotatoria were more abundant in migrating patches, whereas Chironomidae, Ceratopogonidae, Copepoda and Hydrachnidia were more abundant in stationary patches. Body-size structure was affected by sediment migration, with fewer larger organisms in migrating ripples. By modifying the distribution of benthic resources and of meiobenthic consumers, ripple migration likely affects energy flow paths through benthic food webs.