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Abstract Background The integration of organic viticulture practices in grape cultivation represents a pivotal advancement towards sustainable agriculture, emphasizing the importance of environmentally friendly methods that enhance soil health, grape quality, and overall ecosystem biodiversity, thereby contributing significantly to the resilience and long-term sustainability of viticultural ecosystems. This study explored the effects of soil management practices, including chisel, disc harrow, and no tillage, as well as the impact of utilizing Antep radish, broccoli, and olive blackwater as fertilizer applications, on the biochemical composition, specifically biogenic amines (BAs), in the clusters of the 'Royal' grape cultivar within a vineyard setting. Results Throughout the three-year study, no tillage soil management consistently emerged as the most influential soil treatment for enhancing BAs in 'Royal' grape berries, especially in combination with Antep radish and olive blackwater fertilizer applications. Among fertilizer applications, the nontreated control vines consistently had the highest concentrations of critical BAs, such as putrescine, cadaverine, histamine, and dopamine, across different soil management practices. Among the soil management practices and fertilizer applications evaluated, the disc harrow soil management and olive blackwater fertilizer application generally yielded the lowest concentrations of BAs across several metrics.The PCA biplots indicated that experimental years have a similar effect on BA content in grape berries, with specific amines such as serotonin and dopamine being more affected in 2020, while cadaverine, histamine, spermidine, trimethylamine, and norepinephrine were more influenced in 2021, and putrescine, spermine, agmatine, and tryptamine in 2022. Conclusion These findings hold significant implications for organic agriculture, emphasizing the nuanced influence of soil management practices and organic fertilizers on the BA composition of grape berries. Our results indicate the potential of tailored agricultural strategies to enhance plant health and quality, aligning with the principles of sustainability and environmental stewardship inherent to organic farming. Graphical Abstract |