Abstract Little is known about the COVID-19 pandemic-related disruptions in health services and the resilience of the health system response in rural low-resource settings. We conducted a phenomenological qualitative study (October–November 2020) to understand COVID-19-related influences on the utilization and delivery of child health services in Monapo district, rural Mozambique. We interviewed 36 caregivers with children <2.5 years, 21 health providers and 4 district health services staff using in-person in-depth interviews. Data were analysed using inductive thematic content analysis. Our findings showed that caregivers, providers and district health services staff unanimously reported a decrease in child consultations at the start of the pandemic. Administrative data from health facilities confirmed persisting declines in monthly consultations. Respondents explained reductions due to miscommunication about health facility operations, fear of COVID-19, reduced consultation schedules and reduced household incomes. Providers reported several challenges in delivering services including lack of caregiver compliance with risk mitigation measures, caregivers’ fear of risk mitigation measures, perceived lack of caregiver knowledge about COVID-19 and lack of supplies and protective equipment. All respondents described how COVID-19 had increased food insecurity and food prices and reduced incomes and livelihoods. These negative economic consequences were perceived as the main reason for reported increases in cases of child malnutrition. Despite reductions, child health service utilization and delivery have largely continued throughout the COVID-19 pandemic, indicating an adaptive and resilient primary health system response in Monapo district. Our findings highlighted the persistent difficulties providers and caregivers face adhering to COVID-19 prevention and risk mitigation measures. A coordinated multi-sectoral response is needed to address the persistent negative economic impacts of the pandemic for young children and their families in rural areas.