Since leaving politics, Thwaites has become a Professor at Monash University and Chair of its Sustainable Development Institute and ClimateWorks Australia. Thwaites has also been appointed to a number of senior board positions including President, Australian Centre for the Moving Image (ACMI), Chair Australian Building Codes Board, Chair the Climate Group Ltd, Chair Peter Cullen Trust and director Green Building Council of Australia and Fair Trade Australia New Zealand. He was also a consultant to Maddocks Solicitors with specialty areas of practice in environment, water and climate change between 2008 and 2015.