Taking into consideration the altered security landscape in Europe and globally, notably due to the Russian Federation's full-scale aggression against Ukraine, state-sanctioned terrorism, humanitarian and natural disasters, and hybrid challenges, significant increases in security risks for the EU have occurred. As a result of these events, the primary obstacles impeding the EU's attainment of strategic independence have been identified. This article focuses on the European Union's security strategy, namely PESCO and the Strategic Compass, which is one of the main documents governing the security sector. The EU's global security strategy also stresses the importance of reinforcing its defense capabilities. The strategy states that only a strong and unified EU can effectively counter contemporary challenges. The adoption of the Strategic Compass followed comprehensive analyses in the domains of crisis management, resilience, capacity-building, and partnership. The application of the principle of subsidiarity is recommended within its limits. However, clear channels and methods for interaction between various levels, encompassing EU institutions, member states, public and private sectors, as well as civilian and military entities, the EU and NATO, are advised. From a capacity development perspective, there is an emphasis on expanding the complementary relationship between the EU and NATO. The paper aims to examine the effect of these challenges on the EU, as demonstrated in the Global Security Strategy and Strategic Compass of the EU, and the Strategic Concept of NATO. The study's methodology is grounded in the broad research methods of the neo-institutional approach and the analysis of security institutions within the European Union. The results of the research showed that the main challenges to the EU's strategic autonomy are: the difficulties of coordinating the security policies of individual EU members, the difficulties of bridging the gap between their rhetoric and actions, the difficulties of determining Brussels' security priorities and its key projects in this area, where the Union's financial and institutional efforts should be directed, the financial challenges it faces, etc. It is argued that today, given the common security challenges, the coordination of EU and NATO efforts in responding to them is particularly important.