The COVID-19 pandemic has underscored the importance of waste separation for efficient management, disease control, public health protection, and fostering sustainable communities. This study investigates residents’ waste separation behaviour in Nigeria during the pandemic using an extended Theory of Planned Behaviour (TPB) framework. Analyzing data from 726 residents in Lagos and Oyo states, we found that attitude, perceived behavioural control, subjective norms, and intention significantly predict waste separation behaviour, with attitude emerging as the strongest influence. This highlights the crucial role of individual beliefs in shaping waste management practices. Importantly, past waste separation behaviour positively correlates with the intention to separate during public health emergencies. However, perceived policy effectiveness negatively moderates the link between intention and actual separation behaviour. This study suggests strategies for improved biodegradable infectious waste management to support economic activities. More so, Post-COVID-19 pandemic tailored interventions and policies are crucial to enhancing waste separation behaviour, ultimately promoting public health and sustainable communities in Sub-Saharan Africa, for day-to-day environmental safety or preparedness in the event of future health emergencies.