The second year of the MATA programme comprises a high-level internship in an international or national institution, or within the corporate or civil society sector, and one semester of coursework at the partner institution. For students starting at the College of Europe, the internship can be done in semester 3 or 4, and is expected to be completed in the United States or North America; for those who spent their first year at The Fletcher School, the internship has to be done in semester 3, and will normally be completed in Europe prior to a final semester of coursework at the College of Europe.

Past internship placements included: the European Parliament, the European Parliament Liaison Office in Washington, DC, the European Union Delegation to the United Nations in New York City, the US Mission to the EU (Commercial Service) in Brussels, and major think tanks in Washington, DC, such as the Atlantic Council and the Brookings Institution. Several of these internship placements were paid positions. Additionally, thanks to a partnership with the Squire Patton Boggs Foundation, one or two MATA students have each year had the opportunity to benefit from a Squire Patton Boggs Public Policy Fellowship and related grant to complete internships in the non-profit sector.