As a national institution that leads agricultural research, ISABU works closely with other research institutions in the same field, both national, regional and international. In addition, ISABU also collaborates with some donors who finance the activities of its projects.

At the national level, ISABU collaborates with other agricultural research institutions such as the Faculty of Agronomy and the Higher Institute of Agriculture (ISA) of the University of Burundi, the Institute of Agronomic and Zootechnical Research, National Center for Food Processing (CNTA) and the Faculty of Agronomy of the Private University of Ngozi.

At the regional level, ISABU works in partnership with the National Institutes of Agricultural Research of ten Central and Eastern African countries as part of the ASARECA project. Its research programs have for a long time worked closely with 15 regional research networks, namely: EAPGREN, EARRNET, ECABREN, ECAMAW, ECAPAPA, ECARSAM, ECARRN, FOODNET, ECARRN, FOODNET, PRAPACE, PRAPACE, RAIN, RAIN, EARRNET, EARRNET, ECABREN, ECAMAW, ECAPAPA, ECARSAM, ECARRN, FOODNET, PRAPACE, RAIN, PRAPACE, RAIN, RAIN, SWMnet, TOFNET, A-AARNET, BARNESA and AHI.

At the international level, ISABU collaborates with the CIP (in the sanitation of potato crops), the IITA International Center for Research in Tropical Agriculture), CIMMYT (supply of genetic material for cereal crops such as corn and wheat), ICRAF (collaboration in agroforestry), University of Liège and Gembloux and others.

However, it is important to note that most of these networks are no longer functional with the recent restructuring of ASARECA. ISABU receives technical and financial support mainly from ASARECA and donors such as the World Bank, the International Fund for Agricultural Development and Belgian Technical Cooperation. However, 30% of the needs to relaunch and revitalize scientific research activities are covered.

Since 2007, Belgian Technical Cooperation has supported ISABU through the Institutional Support Project, which has just changed its name to become PAIOSA currently. The PAI project supported ISABU in the establishment of a Master Research Plan and a Strategic Plan. It also supported Regional Research Stations, in particular through the construction/rehabilitation of infrastructures.