The need to improve agroecosystem sustainability to secure yields, minimize environmental impacts and improve soil health is widely recognized. Organic production systems are one of the strategies that may be used to alleviate the negative environmental repercussions of conventional agriculture. In the present study, we compared the impact of conventional and organic production systems on the almond (Prunus dulcis (Mill.) D.A. Webb) yield and quality of nuts of two cultivars (Marcona and Desmayo largueta), with both systems being managed on marginal hillslopes in the southeast of Spain. Our findings show that the organic production system in rainfed almond trees has positive effects on certain nut quality parameters, with a slight decrease in almond yield, specifically 9.5% for cv. D. largueta and 1.3% for cv. Marcona, with respect to the conventional system. The results obtained have varied depending on the cultivar. Statistically significant differences have been obtained for cv. Marcona in the sugar content (54.4 and 49.8 g kg−1 in organic and conventional, respectively) and the total phenol content (3.41 and 2.46 g GAE kg−1 for organic and conventional, respectively). In the case of cv D. largueta, statistically significant differences were found between the organic and conventional systems for antioxidant activity (14.8 vs. 8.68 mmol Trolox kg−1, DPPH), fatty acid content (229 vs. 188 g kg−1 dw), saturated fatty acids (36 vs. 28.7 g kg−1 dw), monounsaturated fatty acids (113 vs. 110 g kg−1 dw) and polyunsaturated fatty acids (60.3 vs. 49.6 g kg−1 dw). Here, we show for the first time how a rainfed organic system allows for higher-quality almonds, specifically with a higher content of phytochemicals beneficial for health, which, together with the higher price compared to conventional almonds, could compensate for the yield losses while preserving the sustainability of marginal agroecosystems.