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Summary Restoration of key species in dynamic coastal ecosystems benefits from reduction in environmental stress. This can be realized by promoting positive feedback (intrinsic processes) or by reducing extrinsic negative forcing. In a seagrass (Zostera noltii) restoration project in the south‐western Netherlands, we investigated transplantation success in relation to intrinsic processes (i.e. comparing sods vs. single shoots, transplant size, transplant configuration and transplant density) and extrinsic forcing (i.e. bioturbation by Arenicola marina, desiccation and exposure to water dynamics). In total, 2600 m2 of seagrass sods were mechanically transplanted to six intertidal flats over the course of 5 years. In total, 43% of sod transplants (2·25 m2) survived at the long term, whereas single shoot transplants failed within the first 3 months. The use of larger, or more compact (sod), transplant configurations had no long‐term effect on survival, and initial densities did not affect transplantation success either. Reducing desiccation stress increased the transplantation success during the first growing season. Shielding transplants from bioturbating lugworms had a positive effect on long‐term survival. Seagrass abundance in summer was related to spring abundance, whereas winter survival was not related to prior seagrass abundance. At four of the six intertidal flats, transplants gradually decreased in size over time. At the other two, extensive colonization occurred around the transplant areas in some years and was still partly present in 2015. A correlation with the studied environmental parameters was not found. Synthesis and applications. Intrinsic processes favour transplantation development during the growing season, allowing positive feedback. Extrinsic processes favour the development at a longer time‐scale (i.e. reduction in bioturbation, thus breaking the positive feedback of the bare state). Most surprisingly, the starting colonization of two out of six tidal flats could not be related to environmental factors (hydrodynamics, light, emergence time, sediment characteristics, macro‐algae and grazing). Environmental managers can improve transplantation success by restoring the positive feedback, reducing stress, but also via risk spreading by performing transplants over wider areas. They thereby accept the complexity of processes and unpredictable temporal and spatial variation in which transplantation sites turn out to be successful.