The author looks at the impact of the COVID-19 crises on the European higher education and scientific cooperation programs. During the pandemic the national governments announced strict lockdowns and other protective measures. Free movement across borders was hampered, university campuses mostly closed and many activities put on hold. In these circumstances participants of international exchange programs became particularly vulnerable: some were unable to move to their destination university or institution, others were experiencing difficulties returning to their home countries. Numerous logistical, administrative, health-related and other problems made the situation difficult for the students, professors and researchers, as well and for the staff responsible for the implementation of such programs. In response to this situation, the European Commission and its executive agencies issued guidelines for the participants, extended project deadlines and made other arrangements. At the same time, additional resources were channeled to digital education initiatives and to supporting research aimed at overcoming the pandemic, including diagnostics, treatment and prevention of COVID-19 and other related research fields. In the new program cycle the budget for the EU education and scientific cooperation programs, such as Horizon and Erasmus have been significantly increased and linked to the post-crisis recovery package. A new impulse has been given to the European education area and European research area. The author argues that despite serious problems caused by the pandemic itself and the lockdowns, the crisis became an additional factor for extending higher education and research programs and deepening integration efforts in these areas.