This study examines the post-war energy and fertilizer crises in the European Union (EU) following the Russia–Ukraine conflict, focusing on their impacts on agricultural output, export dynamics, and policy responses. Using panel data for the EU-27 covering 2015–2024, the research employs Difference-in-Differences (DiD) and Triple-Difference (DDD) models complemented by policy scenario simulations to identify causal effects of energy and fertilizer price shocks on agricultural productivity. Results reveal that higher natural gas and fertilizer prices significantly reduce agricultural output, confirming the high dependence of EU agriculture on energy-intensive fertilizer inputs. However, policy interventions under the Common Agricultural Policy (CAP), along with national-level relief measures, substantially moderated these adverse effects. Robustness checks confirm the persistence of these relationships across alternative specifications, lag structures, and sub-sample analyses. The findings underscore that while short-term support mitigated immediate yield and income losses, the EU’s long-term resilience depends on diversifying fertilizer supply chains, promoting green ammonia technologies, and reducing energy dependence through sustainable industrial transitions. The study provides actionable insights for policymakers seeking to align food security, energy security, and climate transition goals within a volatile geopolitical environment.