The history of the Department of Agroecology can be traced back to 1886, when the research stations were managed by the Royal Danish Agricultural Society. Due to public demand, the work was transferred to a govermental institution in 1898.
In the course of time, a large number of research farms were established throughout the country. In addition, the Danish Institute of Plant and Soil Science was established to support the analytical work.
In the beginning of the 1980s the National Institute of Animal Science and the Danish Institute of Plant and Soil Science began collaborating to establish a research facility at Foulum. Later on, the Danish Institute of Plant and Soil Science established a research facility at Flakkebjerg, whereafter agricultural research began to be gathered at these two locations.
In 1997, the National Institute of Animal Science and the Danish Institute of Plant and Soil Science were merged to form the Danish Institute of Agricultural Sciences. In 2007, the institute merged with Aarhus University and the Faculty of Agricultural Sciences was established.
In 2011, the university underwent major restructuring, and the Department of Agroecology became part of the Faculty of Science and Technology.