Agriculture must secure food supply while reducing its pressure on the environment, yet evidence for Central and Eastern Europe, particularly outside the EU and after the 2022 shock, remains limited. This study assesses the eco-efficiency, dematerialisation and decarbonisation of agricultural systems in 11 EU member states, the Republic of Moldova, Serbia and Ukraine over 2000–2023. Using the most recent complete FAOSTAT data (336 country-year observations), it combines a Slacks-Based Measure model with undesirable outputs, a global Malmquist–Luenberger index and the Tapio decoupling elasticity. Non-EU systems, mostly low-input, were, on average, more eco-efficient (0.83 vs. 0.64), but by 2022–2023 both groups had converged at 0.74, as member states improved and non-EU countries deteriorated. Environmentally adjusted productivity grew by almost 1% per year, mainly through technical change in member states. Dematerialisation was selective: land, labour, energy and emission intensities fell, whereas fertiliser intensity rose. Eight countries achieved strong decoupling over the full period, but after 2022 only Czechia and Poland reduced emissions without reducing output. High eco-efficiency in extensive systems does not guarantee resilience; agricultural policies should combine input-use efficiency with investment in technology and adaptation to shocks.