PEI’s principle established interdisciplinary research centers include:

The Carbon Mitigation Initiative is a 15-yearlong partnership among Princeton University and BP with the goal of finding solutions to the carbon and climate problem. The program involves over seventy faculty, research associates and graduate students from the sciences, engineering and policy fields. CMI’s research groups are aligned around projects in climate science, energy technology and carbon capture, carbon storage, and integration and policy.

The Center for BioComplexity, is home to two complementary DARPA projects under the umbrella "Fundamental Laws of Biology," and individually titled: "From microstates to macrodynamics: A new mathematics of biology" and "Predictive Biology: Adaptability, Robustness and the fundamental Laws of Biology." These multi-institutional and multi-disciplinary efforts involve researchers at a number of institutions in the United States and around the world, and disciplines from basic topology to dynamical systems, from cell biology to ecosystem science. Its focus is the development of new mathematical approaches to complexity in biology, looking for both unification and uniqueness across levels of organization.

The Cooperative Institute for Climate Science (CICS) is a collaboration between Princeton University and the National Oceanographic and Atmospheric Administration’s (NOAA) Geophysical Fluid Dynamics Laboratory (GFDL) to carry out basic research in the climate sciences. CICS provides expertise and performs research in the climate sciences including climate change and variability, and biogeochemical cycles.

Research activities of PEI's Energy Systems Analysis Group focus on identifying technologies and policies that could facilitate long-term solutions for major energy-related societal problems -- including global climate change, urban air pollution, energy-import dependence, the risk of nuclear weapons proliferation, and poverty in developing countries.

Managed by the Princeton Environmental Institute (PEI), the Grand Challenges Program was launched in 2007 as a collaboration involving PEI, the Woodrow Wilson School of Public and International Affairs, and the School of Engineering and Applied Science.  The Grand Challenges Initiative is an integrated research and teaching program designed to promote student involvement and faculty research on complex global environmental issues with scientific, technical, public policy, and human dimensions.

The Energy Challenge examines the impact of our energy consumption, and addresses the immediate need to transform the global energy system by engaging research in climate change and its impacts, alternative energy sources, and geopolitical factors such as oil and the Middle East. The cooperative supports projects and courses that address the management of fossil fuels, the expansion of alternative energy sources, and the reduction of energy demand through technological and societal changes.

The Development Challenge focuses on the difficult balance between economic development and natural resource preservation in sub-Saharan Africa. Eliminating poverty among a growing population that survives directly off the fragile land is a vexing challenge, one exacerbated by perennial water scarcity.

The Health Challenge focuses on the complex and pressing problems of infectious disease around the world, and specifically its impact on developing countries. The cooperative bridges the natural and social sciences by examining multiple dimensions of disease ecology, management, treatment, and prevention, and by seeking solutions through scientific, technical, and health policy investigations.