BackgroundThe COVID-19 pandemic has challenged the resilience of Maternal, Neonatal, and Child Health (MNCH) care in Indonesia. Mobility restriction policy and obligatory preventive measures practices could influence the service implementation. Previous literature suggested that communicable diseases outbreak brought fear and mistrust to the health system which resulted in the decrease of service coverage during emergency situations. As one of the world’s worst-hit COVID-19 countries, Indonesia faces considerable challenges in maintaining health services, including MNCH care. This study investigated multi-level factors which become barriers to the implementation of MNCH care during the COVID-19 pandemic in Indonesia.MethodQualitative case study was conducted in three Kabupaten (districts), namely Sidoarjo, Gowa, and Manggarai Barat. The selection of these areas was based on the high COVID-19 cases and different achievements in MNCH indicators’ coverages. Individual in-depth interviews were conducted with 133 people involved in MNCH services, such as women as the main users of the services, health workers, cadres, village representatives, as well as staff from local district health offices. Data were analyzed using the Socio-Ecological Model (SEM) Framework and constant comparative techniques to triangulate information among informants. ResultA total of 133 people participated in the study, of which 67% were women who were pregnant, giving birth, or having children aged under-5 during the COVID-19 pandemic. The factors that affect the utilization of MNCH services were categorized in five socio-ecological levels of analysis, namely individual factors (fear of COVID-19 contraction and awareness of the importance of MNCH services); interpersonal factors (unsupportive extended family and financial barriers); community-based factors (local norms and beliefs, limited transportation services, and geographical barriers), organizational factors (unequal distribution of health resources, ineffective implementation of preventive measures in the health facility, and impractical innovation of services approach), and policy (rapid development of guidelines and ‘one size fits all’ policy issues). ConclusionsFear of COVID-19 contraction and persistent barriers from multi-faceted factors had hindered the effective implementation of MNCH care during the COVID-19 pandemic in Indonesia. The Government of Indonesia, along with local governments, are required to develop specific solutions based on the capacity of health resources as well as interactive and multilevel factors which inhibit women’s decision and practice to seek MNCH care in a volatile situation.