The ongoing COVID-19 pandemic has posed new and has aggravated already existing public health challenges in Malawi and worldwide. Having a better understanding of these challenges can help facilitate the identification of solutions and designing further public health interventions and policies for effective management of the COVID-19 pandemic. This article presents an overview of the situation of COVID-19 in Malawi and identifies emerging public health challenges that the country is facing amidst this pandemic. It is based on a review of relevant key policy documents, reports, and publications. Some of the key emerging challenges identified in Malawi are worsening population health and socio-economic status; health system challenges like inadequate financing and human resources, disruption of essential health services; a rise in mental health conditions and suicide rates; teenage pregnancies and early marriages; and changes in some health policies. The findings point to the need to invest more in strategies for health promotion, health system strengthening and avoiding disruptions and recovery of services. These should include COVID-19 vaccination promotion campaigns, improvement of the public health surveillance system, strengthening the health workforce, implementation of health financing strategies, procurement of adequate essential medicines and supplies, and strengthening of youth-friendly reproductive health services, community health services and community engagement. These will ensure that the health system in Malawi is well-equipped to deliver resilient, sustainable and quality health services amidst and beyond the COVID-19 pandemic thereby promoting progress toward the achievement of Universal Health Coverage (UHC) and Sustainable Development Goals (SDGs) in Malawi.