Malawi faces increasing pressure on forest resources as rising urban demand for charcoal and firewood accelerates forest degradation in the Lilongwe River Upper Catchment, the primary water source for Lilongwe City. With over 90% of Malawians dependent on biomass energy and the country losing an estimated 33,000 hectares of forest annually, the consequences for water security, soil integrity, and rural livelihoods are severe. Existing research has largely examined woodfuel governance as a social and institutional issue, emphasising policy failures, corruption, and weak enforcement, with limited attention to the biophysical processes through which governance decisions shape landscapes. In this context, tracking changes in soils, water flows, and vegetation dynamics offers an important complementary perspective critical for integrated interventions. This paper proposes a conceptual framework, a Critical Zone Science and Social–Ecological Systems (CZS-SES) framework, which allows examination of how governance systems interact with biophysical processes across scales. The framework, informed by synthesis of policy documents and the empirical literature, highlights the need for more integrated, multidisciplinary approaches to understanding woodfuel governance and its implications for habitability in Malawi and across Africa.