AbstractMicrophytobenthos (MPB) resuspension is a key mechanism in the transfer of organic matter from productive intertidal mudflats to terrestrial and marine systems. In this study, we infer on the contribution of physical and biological factors involved in the MPB resuspension. We use a physical‐biological coupled model forced by realistic meteorological and hydrodynamical forcings to simulate chronic (without any concomitant sediment resuspension) and massive (driven by bed failure) resuspension over a year. The model simulates mud surface temperature, MPB growth, and grazing by the gastropod Peringia ulvae. The model suggests that MPB resuspension is the highest in spring tides and at the flood beginning due to high current velocity and low water heights that promote waves‐sea bottom interactions. The seasonal export of MPB biomass is the highest in spring, up to threefold higher than in summer when the export is the lowest. The simulated seasonal dynamics of MPB resuspension results from the MPB biomass concentration in the sediment, physical disturbances, and the bioturbation activity by P. ulvae. Annually, 43% of the simulated MPB primary production is resuspended. The MPB resuspension (60.8 g C·m−2·yr−1) exceeds the loss by P. ulvae grazing (41.1 g C·m−2·yr−1). The model suggests that chronic and massive resuspension events are important in the synoptic to seasonal MPB dynamics in temperate intertidal mudflats. Accounting for such processes in the carbon budget assessment in the land‐ocean interface could bring new insights to our understanding of the role played by MPB in the coastal carbon cycle.