BackgroundImproving health system performance depends on the quality of health policy implementation at the local level. However, in general, the attention of researchers is mainly directed towards issues of health policy design and evaluation rather than implementation at the local level. The management of the COVID-19 crisis, especially in Europe, has particularly highlighted the complexity of implementing health policies, decided at the national or supranational level, at the local level.MethodsWe conducted 23 semi-structured interviews with the main stakeholders in the management of the COVID-19 crisis in the second largest French region in order to identify the different actors and modes of coordination of the local implementation of health policies that this crisis management illustrates in a very visible way. Our methodology is complemented by a content analysis of the main guidelines and decisions related to this implementation.ResultsThe analysis of these data allows us to identify three levels of implementation of health policies at the local level (administrative, organizational and operational). Interviews also reveal the existence of different types of coordination specific to each of these levels of local implementation of health policies. These results then make it possible to identify important managerial avenues for promoting global coordination of these three levels of implementation.ConclusionsAlthough research on health services emphasizes the existence of several levels of local implementation of health policies, it offers little in the way of definition or characterization of these levels. The identification in this study of the three levels of local implementation of health policies and their specific forms of coordination contribute to a more precise characterization of this implementation in order to promote, in practice, its global coordination.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13012-023-01277-0.