Melkassa Agricultural Research Center (MARC) was established on 17 June 1969 as a National Horticultural Research Station in Adama town with five expatriates and thirty Ethiopians with one vehicle to experiment on five hectares of land. The Center was moved to the current place, Melkassa, in search of irrigation water and more spaces in 1983. The aim of the center at its establishment was to coordinate varietal improvement research of horticultural crops that were situated across different locations (Werer, Koka, Jimma and Bako) in Ethiopia. In the early 1970s, additional research programs were included. Lowland Pulse research was a pioneer program established to coordinate the lowland pulses research across the country. Sorghum research program was the third commodity to be included into the center following the establishment of the Ethiopian Sorghum Improvement Project (ESIP) in 1972, which was considered as the landmark for the establishment of formal research on sorghum in Ethiopia.

In 1982, ESIP integrated to the EIAR (the then IAR) and founded as one of the national programs to lead sorghum research based at MARC. In the same year, research in Agricultural Mechanization was launched. Similarly, sericulture technology got attention by the EIAR (the then IAR) in the mid-1970s as a component of coffee diversification following the sudden outbreak of coffee berry disease (CBD) and the devastation of coffee plantation in the country. The program was subsequently discontinued in the late 1980s due to priority concerns. However, the importance of the program was reconsidered and reinitiated in 2000 at MARC. Over the years, the center accommodated Natural Resource Management, Lowland Maize Research, cross cutting departments such as Agricultural Economics, Agricultural Extension, Food Science, Crop Protection, Agronomy and physiology, 2nd Plant Biotechnology researches.