The Schengen system, as one of the fundamental pillars of European integration and freedom of movement within the European Union, faces growing and complex challenges in the context of non-traditional security threats. The foundation of the Schengen area is the opening of the internal border, and in such an area, cross-border threats affecting internal security are of common interest to all member states. Non-traditional security threats know no borders and as such represent a complex challenge that requires the joint action of all members with the aim of creating a secure environment. Terrorism has spread as a global threat that knows no borders, organized crime uses highly sophisticated techniques and networks, crosses national borders to smuggle people, weapons, drugs and other illegal goods. Mass migration, fueled by geopolitical instability and economic inequality, poses a challenge to the Schengen system due to its potential impact on social cohesion, the economy and overall security. Cyber threats, global trafficking in people and narcotics further complicate the situation, spreading and increasing the rates of crime and human rights abuses. The paper describes the fundamental values on which the Schengen area was established and highlights the significant challenges that the Schengen system has faced in a relatively short time frame, especially with regard to the migrant crisis and COVID-19. Over the years, the European Union and its members have made great joint efforts to respond to all the challenges posed. Although they successfully overcame the crises, it is increasingly clear that increased cooperation, upgrading of infrastructure and better organization at the collective level of all member states are necessary for the sustainable preservation of security within the Schengen area.