Students of the MATA programme write a Master's Thesis (25 ECTS) on a topic related to transatlantic affairs. The thesis is co-supervised by a member of the College of Europe and a member of the Fletcher School faculty. 

The best Master’s Thesis submitted by a MATA student receives the ‘Jan Olaf Hausotter Memorial Prize for the Best Thesis in Transatlantic Affairs’. Jan Olaf HAUSOTTER was an alumnus of the College of Europe (Bertha von Suttner promotion, 2002-2003) and a graduate of The Fletcher School of Law and Diplomacy. He was working as a Political Affairs Officer for the UN Stabilization Mission in Haiti when he was killed during the 2010 earthquake. The prize is sponsored by his former classmates of the Bertha von Suttner promotion and awarded on the occasion of the Closing Ceremony of the College of Europe in Bruges.

The best thesis prize from the 2023-2025 promotion was awarded to Juliette Perrier and Aidan Kelly. Juliette Perrier worte the thesis, 'Sub-Atlantic: Navigating American-European undersea internet infrastructure security and resilience through joint EU, US and NATO fora, initiatives and feasibility'. Aidan Kelly wrote the thesis, 'Sovereignty under attack? Secrecy jurisdictions, free-trade zones, and the 'commercialization of sovereignty'.