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Migrating bedforms have high levels of particulate organic matter and high rates of pore water exchange, causing them to be proposed as hot spots of carbon turnover in rivers. Yet, the shifting of sediments and associated mechanical disturbance within migrating bedforms, such as ripples, may stress and abrade microbial communities, reducing their activity. In a microcosm experiment, we replicated the mechanical disturbances caused by the periodic sediment shift within ripples under oligotrophic conditions. We assessed the effects on fungal and bacterial biomass ratio (F:B), microbial community respiration (CR), and bacterial production (BCP) and compared with stable undisturbed sediments. Interactions between periodic mechanical disturbance and sediment-associated particulate organic matter (POM) were tested by enriching sediments collected from migrating ripples with different qualities of POM (fish feces, leaf litter fragments and no addition treatments). F: B and BCP were affected by an interaction between mechanical disturbance and POM quality. Fish feces enriched sediments showed increased F: B and BCP compared to sediments with lower POM quality and responded with a decrease of F: B and BCP to sediment disturbance. In the other POM treatments F: B and BCP were not affected by disturbance. Microbial respiration was however reduced by mechanical disturbance to similar low activity levels regardless of POM qualities added, whereas fish feces enriched sediment showed short temporary boost of CR. With the worldwide proliferation of migrating sand ripples due to massive catchment erosion, suppressed mineralization of POM will increasingly affect stream metabolism, downstream transport of POM and carbon cycling from reach to catchment scale.