In 2021, Lithuania had to deal with a massive irregular migrant crisis artificially created by the Belarusian regime using migrants as political pressure. On the Belarusian side, the organised flows of migrants, mainly from the Middle East, threatened Lithuania’s national security, and the security and defence institutions had to take action, including military engagement, to reinforce the capacities of the civilian institutions. This case study examines good practices and challenges in cooperation between the military and the internal affairs system. The case demonstrates that effective inter-institutional cooperation and military engagement can significantly enhance a country’s ability to respond to complex hybrid threats. The successful use of military-specific know-how, effective inter-institutional information sharing, and the establishment of a single channel of communication have enabled timely decision-making and a coordinated response to the crisis. However, smooth cooperation was challenged by differences in organisational cultures between civilian and military institutions in terms of levels of authority and jurisdiction, as well as by the need to ensure that the long-term involvement of the military did not adversely affect the military training processes. These good practices can be of value to other countries seeking to strengthen their capacity to anticipate, respond to, and mitigate future crises, thus ensuring the security of their citizens and building resilience to external threats. The lessons learned from the Lithuanian experience underscore the importance of robust civil-military cooperation and the development of flexible institutional frameworks that can effectively address emerging security threats in different geopolitical contexts. This is particularly important in view of the growing number of hybrid threats, where military engagement is required as a backup for civilian institutions.