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Greenhouse gas (GHG) emissions are influenced by physical, chemical, biological, and anthropogenic factors. The objective of the study is to carry out a comprehensive analysis of the emissions of three important agricultural GHGs (CO2, N2O, and CH4) in both rows and alleys of a vineyard (1) and to understand their interactions with the agricultural operations carried out in the experimental plot, namely tillage, inter-row management, application of mineral and organic fertilizers, and irrigation and pruning, as well as the agroclimatic conditions of the plot (2). The study was conducted in a vineyard of Vitis vinifera L. cv. Tempranillo blanco in the DOCa. Rioja grape-growing region, during 2017, 2018, and 2019. Cumulative CO2 emissions were highest in 2018, reaching 934.7 ± 66.5 kg ha−1 day−1 in the alleys and 926.8 ± 76.5 kg ha−1 day−1 in the rows, in agreement with the wetter year and organic matter decomposition at the end of 2017. N2O emissions during the three-year study were mainly affected by mineral fertilizer application, with increases of 41.1 g ha−1 day−1 in the alleys and 49.3 g ha−1 day−1 in the rows during 2018, and 33.1 g ha−1 day−1 in the alleys and 39.6 g ha−1 day−1 in the rows in 2019. Regarding CH4, anaerobic soil conditions in 2018 (the year with the highest rainfall) led to the highest flux of CH4 emissions to the atmosphere, with 215.5 ± 51.0 g ha−1 day−1 in the corridors and 238.4 ± 54.9 g ha−1 day−1 in the rows. This study emphasizes the complex interplay of physical, chemical, biological, and human-related factors affecting GHG emissions in viticultural soils. Understanding these dynamics is essential for developing sustainable vineyard practices that minimize emissions and contribute to climate change mitigation.