The AEI is part of the governing bodies of a large number of European programs co-financed by the European Commission that follow the ERANET COFUND schemes, Art. 185, Art. 187 (coordination networks, which constitute the instrument to launch transnational calls for projects ), participating basically as a funding body.

The main mission of the AEI representatives in these consortia is to define the themes of the transnational calls in accordance with the priorities and needs of the SECTI, as well as to promote, as far as possible, the alignment of national requirements and procedures and international

The AEI has participated in more than 50 joint calls within the framework of Horizon 2020, in the fields of health, bioeconomy, materials, information sciences, environmental sciences, energy and social sciences and humanities, among others, financing more than 500 projects research.

Since 2018, the AEI has financed Spanish groups with the R+D+i project instrument "International Joint Programming" which, since 2020, consists of a direct concession resolution, in accordance with the third final provision of the Royal Decree-Law 23/2020, of June 23.

The Agency's participation in joint programs of various schemes generates, directly or indirectly, a return to the SECTI as a whole of around 5 million euros per year.

The AEI finances Spanish groups with the International Collaboration Projects (PCI) instrument. Since 2020, the instrument consists of a direct concession resolution, in accordance with the third final provision of Royal Decree-Law 23/2020, of June 23. The tools prior to PCI were the International Joint Programming calls.

The PCI application application is opened several times a year in order to keep track of the results of international calls.