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Cover crops (CCs) are widely promoted as a cornerstone of climate-smart and diversified agriculture, yet their effectiveness remains highly context-dependent. Here, we present a coherent, multi-faceted framework for understanding when, where, and how CCs can deliver net climate and productivity benefits. First, drawing on a global meta-analysis of over 2,300 observations, we demonstrate that CCs can substantially enhance agroecosystem multifunctionality—including crop yield, soil carbon storage, and erosion control—when practices are optimized. Long-term implementation, climate-smart management (e.g. no-tillage), and diversified CC mixtures emerge as key determinants of synergistic outcomes, particularly in environmentally constrained regions. Second, we show that these benefits are frequently constrained by a climate–productivity trade-off driven by elevated nitrous oxide (N2O) emissions. By integrating multiple global meta-analyses with machine-learning approaches, we identify aridity and soil acidity as dominant controls of this trade-off through their influence on microbial nitrogen cycling. Region-specific optimization of nitrogen inputs can substantially reduce trade-off intensity, mitigating up to ~2.65% of global crop-specific N2O emissions while sustaining yield gains, especially in semi-arid alkaline systems. Finally, moving beyond CCs as a standalone solution, we explore the potential of coupling CCs with enhanced rock weathering (ERW) as a complementary nature-based strategy. Evidence from systematic reviews and field observations suggests that CC–ERW synergies can improve biogeochemical synchrony, strengthen soil food webs, and further reconcile climate mitigation with agricultural productivity. Together, these findings highlight a pathway from practice optimization to system-level integration for building resilient, multifunctional agroecosystems under climate change.