Policy siloes between national adaptation plans (NAPs), nationally determined contributions (NDCs) and sustainable development hinder effective climate action and resource governance in East Africa. Further, rapid population growth and climate change impacts intensify demands for water, energy, and food (WEF), fuelling resource exploitation. This study employs a mixed-qualitative methodology using document analysis, and semi-structured interviews to examine the interlinkages between NAPs, NDC and regional development priorities. Results show implied connections between policy instruments, sustainable development, and climate action form the crux of WEF interlinkages. In practice, incoherence between these instruments create competition and trade-offs that increase WEF resource security. For example, the focus on food security, mostly through extensification, has created tradeoffs with water and energy security, undermining development goals. There are implicit interlinkages in policy and, to a certain extent, in practice. Although insufficient, these are foundations for a bottom-up approach to implementing integrated climate action commitments. Understanding the interconnectedness and interdependencies between sector policies, climate actions, and supranational development plans could catalyse and accelerate sustainable development while building resilience, through a multi-sectoral approach. We posit the need for a transdisciplinary, WEF approach to catalyse cooperation for development and climate action in East Africa. Ultimately, a transdisciplinary approach focused on equity, social justice, sustainability, and a just transition is required to support development agendas.