ATREE's organisational structure is designed to promote creative interdisciplinary approaches that integrate research with policy and action in addressing key environmental problems. Two Centres with four nested Programmes, and an Academy provide ATREE the necessary structure to conduct insightful research that fuels its 'think-tank' and drives its capacity building activities.

The Suri Sehgal Centre for Biodiversity and Conservation and Centre for Environment and Development are the two Centres that represent the broad thematic areas under which are nested the four cohesive inter-linked programmes. Each programme envisions integrating research with policy impacts and active engagement with society, and contributing to the pedagogic activities of the Academy for Conservation Science and Sustainability Studies. Climate Change and governance are broad and essential cross-cutting themes across the four programmes.

The Academy houses a Ph D programme in conservation and development. ATREE's postdoctoral programme offers interdisciplinary coursework that addresses the natural science as well as social science components of conservation and development studies. The Academy also provides certificate courses, training modules and workshops for a broad spectrum of stakeholders.

The Academy has a strong presence in the field through its six field academies or Community-based Conservation Centres. These champion community interactions that advance reciprocal learning and environmental governance in the local landscapes.