Marine habitat function has been typically investigated in terms of biogeochemical regulation but rarely in terms of population renewal, which is mainly controlled by recruitment dynamics. The recruitment phase is crucial for organisms with a bentho-pelagic life cycle, such as bivalves, and it regulates the population renewal success. This study provides new insight on the role of temperate benthic habitats on bivalve recruitment, as a function of nursery areas. Six dominant benthic habitats of the Chausey archipelago (Normandy, France) were studied. In each habitat, bivalve recruit assemblages were described at the end of two reproductive seasons. Furthermore, Ostrea edulis juveniles were immerged on each habitat during two months to compare growth performances and feeding status, estimated by fatty acid composition. Recruit assemblages differ from each habitat according to sediment grain-size composition and bathymetrical levels. Subtidal habitats, and especially Crepidula fornicata banks and Glycymeris glycymeris coarse sands, supported the highest species abundance and richness of recruits. All O. edulis juveniles fed on the same trophic resources but digestive glands of juveniles from C. fornicata banks were more concentrated in total fatty acids than those from subtidal G. glycymeris coarse sands and maerl banks. Our results depict the key role of subtidal and structured habitats, composed of ecosystem engineers, in enhancing bivalve recruitment and extending the bivalve population renewal. This study suggests that the crucial role of these habitats as bivalve nurseries must be integrated in management perspectives.