PURPOSE: The COVID-19 pandemic has had a disruptive effect on the health system. Health facility leaders were at the forefront of maintaining service delivery and were exposed to varied stressors in the early phase of the pandemic. This study aims to explore the leadership experiences of health facility leaders during the early phase of the COVID-19 pandemic in Nigeria's epicentre. DESIGN/METHODOLOGY/APPROACH: This study conducted an exploratory descriptive qualitative study. To achieve this, 33 health facility leaders of different cadres across primary, secondary, and tertiary levels of the public health care system in Lagos, Nigeria, were remotely interviewed. The key informant interviews were transcribed verbatim and were analysed by using thematic analysis. FINDINGS: The health facility leaders experienced heightened levels of fear, anxiety and stressors during the early phase of the pandemic. They also had genuine concerns about exposing their family members to the virus and had to manage some health-care workers who were afraid for their lives and reluctant. Coping mechanisms included psychological and social support, innovative hygiene measures at health facility and at home, training and staff welfare in more ways than usual. They were motivated to continue rendering services during the crisis because of their passion, their calling, the Hippocratic oath and support from the State government. ORIGINALITY/VALUE: The experiences of health facility leaders from different parts of the world have been documented. However, to the best of the authors' knowledge, this is one of the first studies that specifically report multi-layer leadership experiences of health facility leaders during the early phase of the COVID-19 pandemic in sub-Saharan Africa.