The Faculty of Agroindustry (FAi) was established based on the Rector's Decree Number: 06/SK/Rek/IV/2008 dated April 5, 2008, concerning the establishment of the Faculty of Agroindustry (FAi). The Faculty of Agroindustry is a merger of two faculties: the Faculty of Agriculture and the Faculty of Agricultural Technology. Both faculties have been in existence since October 1, 1986, under the auspices of Wangsa Manggala University. The pioneers of the establishment of the Faculty of Agriculture and the Faculty of Agricultural Technology at Wangsa Manggala University at that time were Mr. Ir. Hendro Pawoko Sayid from the Faculty of Agricultural Technology and Mr. Ir. Sugiarto, MS, assisted by lecturers from Gadjah Mada University until they obtained equal accreditation status.

In subsequent developments, on April 5, 2008, in accordance with the Decree of the Chairman of the Wangsamanggala Foundation Number: 02/SKEP/Ket/YWM/IV/2008, Wangsa Manggala University changed its name to Mercu Buana University Yogyakarta (UMB Yogyakarta). This name change was further confirmed by the Decree of the Minister of National Education of the Republic of Indonesia Number 102/D/O/2008 dated June 12, 2008. Along with the name change of the university, a merger of two faculties, namely the Faculty of Agriculture and the Faculty of Agricultural Technology, was also carried out to form the Faculty of Agroindustry (FAi) with three study programs: Agrotechnology, Animal Science, and Agricultural Product Technology. This merger was based on the consideration of the importance of an integrated agricultural mindset in every effort to develop agriculture and its processing technology.

At its inception, the Faculty of Agroindustry UMBY was the only faculty offering three study programs in the field of agriculture within a single management unit: the Agrotechnology Study Program, the Animal Science Study Program, and the Agricultural Product Technology Study Program. Based on the evaluation of internal and external conditions in 2017, a Master's Program in Food Science was opened, conducted based on the Decree for the Opening of Study Programs No. 521/KPT/I/2017. The FAi has lecturers who hold doctoral degrees, and there are already two lecturers with the academic title of professor, making it very adequate to provide master's level education in food science for the community, especially for professionals such as government staff, vocational school teachers, and industry workers. In its development, of the four study programs managed by FAi, three undergraduate programs have been accredited with an A rating by the National Accreditation Board for Higher Education (BAN PT), and the Master's Program in Food Science received a good accreditation rating in 2021.