This research protocol outlines a mixed-methods study assessing two critical environmental stressors in South Sudan from 2021 to 2026: urban heat stress in Juba and recurrent flooding in Jonglei State. It analyses their compound impacts on community resilience. The central objective is to generate spatially explicit, evidence-based knowledge on exposure and vulnerability, with a specific focus on energy infrastructure and household energy security as critical, yet understudied, determinants of adaptive capacity. Methodologically, the study integrates satellite-derived land surface temperature and flood inundation mapping with field-based socio-ecological surveys and key informant interviews within purposively selected communities. A preliminary analysis of 2021–2023 data reveals a concerning intensification of the urban heat island effect in Juba and identifies flood-prone settlements in Jonglei with severely limited access to resilient energy sources for coping and recovery. The significance of this work lies in its integrated, place-based approach, which prioritises African-centred evidence generation and addresses a notable research gap. The anticipated findings will directly inform the development of context-specific climate adaptation strategies, particularly in designing robust energy systems that enhance community resilience against escalating thermal and hydrological extremes. This protocol establishes a rigorous framework for actionable science in a data-scarce region facing profound climate risks.