<p>In arid areas, trends in new farming systems have shifted towards organic farming to promote added-value products and enhance the net incomes of small farmers. In this context, organic and conventional farming systems were investigated to check their impact on pistachio nut quality and mycotoxin contamination. Private rain-fed and irrigated orchards, planted with the main local cultivar Mateur, were selected for each farming system in the Central Eastern Tunisia. Physical traits, oil content (OC), fatty acid composition (FAC), total antioxidant capacity (DPPH), total phenolics content (TPC), total flavonoids (TFC), presence of mycotoxigenic fungi, and subsequent mycotoxins were determined for two successive years. Water supply affected nut and kernel physical traits harvested under organic and conventional farming systems. Both farming systems yielded the highest nut and kernel weight and size and split rate under irrigated conditions. Rain-fed conditions affected the OC, with the highest value in 2017 for both organic and conventional systems. Additionally, FAC varied by farming system, exhibiting year-to-year fluctuations. Irrigated organic farming system demonstrated the highest content of major fatty acids in kernel oil, while TPC and TFC were not significantly influenced by the farming systems. Importantly, no mycotoxigenic fungi or mycotoxin contamination were detected. In conclusion, irrigated farming systems improved the physical traits of nuts, as well as DPPH, OC, and FAC. Organic farming was found to be a viable agricultural system that promotes food safety. Overall, the grower's horticultural practices in both organic and conventional systems had a minimal impact on nut quality deterioration at harvest, making the nuts safe for human consumption.</p>