The implementation of soil conservation measures is essential to promote sustainable crop production in the Mediterranean region. In an organic rainfed almond orchard located in Lanjarón (SE, Spain), a study carried out during 2016–2021 analyzed the influence of different soil management strategies (SMSs) (TT, traditional tillage; NT, no tillage; VF, cover of Vicia faba; VS, cover of Vicia sativa; VS-VE, cover of Vicia sativa and Vicia ervilia) on some selected physical (bulk density, available water content, and aggregate stability), chemical (pH, electrical conductivity, soil-organic content, N, P, K, and micronutrients), and biological (microbial activity) soil properties, relevant to soil health, and their implications for yield and almond quality (physical and chemical). Our results showed that the SMS with legume cover improves soil properties, which had a favorable effect on soil health. The mean almond yield was not significantly affected by the SMS applied, being 315.9, 256.4, 229.1, 212.5, and 176.6 kg ha−1 year−1 for TT, VF, VS-VE, VS, and NT, respectively. Regarding the almond nut quality, the strategy based on implementation of legume cover increased the almond antioxidant activity and the total polyphenol content, which would improve their nutritional value. Here we showed how the use of sustainable SMSs improved the soil properties compared to traditional tillage in rainfed organic almonds, allowing the long-term sustainability of agroecosystems while at the same time obtaining higher nutritional quality almonds.