The Institute of Agricultural and Environmental Sciences began operating on 1 January 2005. It was one of five institutes established as part of the structural reform of the Estonian Agricultural University. IAES continued the work of six former units: the Faculty of Agronomy of the Estonian Agricultural University, the Institute of Experimental Biology, the Institute of Environmental Protection, Polli Horticultural Institute, the Institute of Zoology and Botany, and the EVIKA Plant Biotechnology Research Centre.
In September 2017, a structural reform took effect at the Estonian University of Life Sciences, replacing the former departments with academic chairs. Following the reform, IAES comprised eight chairs and two separate units: Polli Horticultural Research Centre and Rõhu Experimental Station.
Under the academic structure reform that took effect on 1 January 2022, the Institute of Agricultural and Environmental Sciences and the Institute of Economics and Social Sciences were merged. The merged institute retained the name Institute of Agricultural and Environmental Sciences. The existing eight chairs of IAES remained, while the Chair of Rural Economics was added from the Institute of Economics and Social Sciences. This increased the number of chairs at the institute to nine.
At the end of 2025, it was decided to divide the Chair of Crop Science and Plant Biology into two separate chairs. Since January 2026, the former chair has been replaced by the Chair of Crop Science and the Chair of Plant Biology and Field Crop Production.
Today, IAES brings together teaching and research in agriculture, rural economics, environmental protection and biodiversity. The institute comprises ten chairs. Their work is supported by Polli Horticultural Research Centre, Rõhu Experimental Station, the Võrtsjärv Study Centre and the Natural History Collections.
