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In semi-arid vineyard agroecosystems, highly vulnerable in the context of climate change, the soil organic matter (OM) content is crucial to the improvement of soil fertility and grape productivity. The impact of OM, from compost and animal manure, on soil properties (e.g., pH, oxidisable organic C, organic N, NH₄⁺-N and NO₃⁻-N), grape yield and direct greenhouse gas (GHG) emission in vineyards was assessed. For this purpose, two wine grape varieties were chosen and managed differently: with a rain-fed non-trellising vineyard of Monastrell, a drip-irrigated trellising vineyard of Monastrell and a drip-irrigated trellising vineyard of Cabernet Sauvignon. The studied fertiliser treatments were without organic amendments (C), sheep/goat manure (SGM) and distillery organic waste compost (DC). The SGM and DC treatments were applied at a rate of 4600 kg ha⁻¹ (fresh weight, FW) and 5000 kg ha⁻¹ FW, respectively. The use of organic amendments improved soil fertility and grape yield, especially in the drip-irrigated trellising vineyards. Increased CO₂ emissions were coincident with higher grape yields and manure application (maximum CO₂ emissions = 1518 mg C-CO₂ m⁻² d⁻¹). In contrast, N₂O emissions, mainly produced through nitrification, were decreased in the plots showing higher grape production (minimum N₂O emissions = −0.090 mg N₂O-N m⁻² d⁻¹). In all plots, the CH₄ fluxes were negative during most of the experiment (−1.073−0.403 mg CH₄-C m⁻² d⁻¹), indicating that these ecosystems can represent a significant sink for atmospheric CH₄. According to our results, the optimal vineyard management, considering soil properties, yield and GHG mitigation together, was the use of compost in a drip-irrigated trellising vineyard with the grape variety Monastrell.