Purpose The COVID-19 pandemic has made humanity contend with the negative footprint of its activities in which social justice, ecological integrity and economic stability are compromised. This study aims to investigate the impact of COVID-19 on the operation and management of non-governmental organisations (NGOs) in Nigeria. Design/methodology/approach Multiple case study research design was used in the study with interviews from 25 senior-level management staff of NGOs. Findings The analysis revealed that COVID-19 impacts NGOs both negatively and positively. Dominant among the negative impacts are a decline in health-seeking behaviours, low programme implementation, increased cost and wastages resulting from PPE, transition to virtual meetings, a decline in capacity building and staff burnout/pressure. However, some positive impacts include increased efficiency through the use of virtual innovations, peer-to-peer intervention through the establishment of networks, flexibility and prompt adaptation to the crisis, prudent management of available resources, etc. This research contributes to theory and practice. Research limitations/implications Conducting this research and recruiting participants at the height of COVID-19 in Nigeria, in adherence to the prevention guidelines, constituted a considerable limitation to the study. Practical implications Although the identified impact could be useful in framing operational policies and guidelines, the study highlights a salient future outlook with policy implications for both the governance of NGOs and the facilitation of sustainable development goals by the government. Originality/value Although researchers continue to explore the impact of COVID-19, none has considered the NGO sector, especially in developing countries, and with a focus on providing evidence-backed resilience practices for the future.