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Cover crops are increasingly promoted as a management strategy to enhance soil carbon (C) stocks and soil health, but their effects on greenhouse gas (GHG) emissions remain uncertain, particularly in flooded rice systems where anaerobic conditions prevail. In these systems, organic inputs such as green manures have been widely reported to stimulate methane (CH₄) emissions, raising concerns about their net climate impact.Here, we evaluated the impacts of contrasting rice rotational strategies, i.e., winter fallow, hairy vetch (Vicia villosa Roth), and Italian ryegrass (Lolium multiflorum Lam.), on soil health, C dynamics, and GHG emissions in a Mediterranean rice system located in the Ebro Delta (NE Spain). The field experiment was established in 2021, and the results presented here cover the period from February 2024 to October 2025.Soil biological health was assessed by integrating weekly measurements of CH₄ and nitrous oxide (N₂O) emissions with microbial biomass C and nitrogen (N) and litter decomposition of cover crop shoots and roots assessed at key stages of the rice growing cycle. These indicators were complemented by measurements of soil organic carbon (SOC) stocks and soil aggregation to evaluate links between biological activity, soil structure, and C storage. Ongoing analyses of microbial necromass and SOC fractionation into particulate and mineral-associated pools will provide further mechanistic insight into C stabilization processes under different cover crop strategies.Cover crop identity strongly influenced biogeochemical dynamics. CH₄ emissions peaked under vetch during the flooded cultivation phase, whereas no significant treatment effects were detected for N₂O emissions, despite a tendency towards lower emissions under vetch. Consequently, no net differences in global warming potential were observed among treatments. Shoot litter decomposition was significantly slower for vetch than for ryegrass, a pattern not mirrored in roots, and consistent with differences in residue lignin content. However, rapid mass loss occurred for both residue types under anaerobic conditions, suggesting an important role of solubilization processes. SOC stocks did not differ among treatments in the most superficial soil layer, but ryegrass was associated with significantly lower stocks in the 10–30 cm soil layer. Cover cropping tended to promote macroaggregate formation, suggesting potential improvements in soil structure and physical protection of organic matter. Microbial biomass C and N were marginally higher under vetch in autumn, indicating enhanced soil biological activity. At the agronomic level, rice grain yield showed a marginal increase under vetch.Overall, our results suggest that vetch represents a promising cover crop option in Mediterranean rice paddies, enhancing soil biological functioning and rice productivity while not leading to clear increases in total GHG emissions. AcknowledgementsThis study was funded by The Government of Catalonia through the projects AgriCarboniCat and Carboni al Sòl.