From 1991 our educational institution was called the Estonian Agricultural University. New specialities like Environmental Protection, Landscape Architecture, Production and Marketing of Agricultural Products, Landscape Protection and Preservation, Applied Hydrobiology, Environmental Economics and Natural Resources Management were adopted.
In 1996 the new MainBuilding in the outskirts of the town was completed and the administration together with the Institute of Economics and Social Sciences moved in. May 2000 saw the opening of the library, café and canteen in the MainBuilding. In 2004 the new building of Veterinary Medicine and Animal Sciences (Zoomedicum) was opened.
Till the end of 2004 the University had six faculties (Agronomy, Agricultural Engineering, Economics & Social Sciences, Forestry, Rural Engineering, and Veterinary Sciences) and eight institutes (Estonian Agribiocentre, Estonian Plant Biotechnology Research Institute EVIKA, Forest Research Institute, Institute of Animal Science, Institute of Environmental Protection, Institute of Experimental Biology, Institute of Zoology and Botany and Polli Institute of Horticulture).