Citrus crop management has evolved to improve the quality of orchards and production, encompassing agroforestry and agroecological management practices. We sought to analyze different management systems in different seasons of the year, evaluating the quality of the soil physical, chemicals and biological properties, and the herbaceous vegetation occurring in citrus orchards. Five sites were studied: citrus in agroforestry and biodynamic systems (Cs), citrus in biodynamic systems (Co), citrus in conventional systems (Cc), and two forest sites, one with 40 (F40) and another with 200 years of regeneration (F200). Soil properties were evaluated in three layers (0–5, 5–20, and 20–40 cm) in four seasons, while the herbaceous survey was carried out in two of these seasons. The results showed that the Co and Cs orchards had better indicators in terms of chemical (pH, phosphorus, cation exchange capacity, and soil organic carbon (SOC)), physical (soil density, total porosity, and macro- and microporosity), and biological properties (global enzymatic activity) than the Cc management. The agroforestry management was even superior in soil quality, with improved pH levels, microporosity, and feeding behavior of the soil fauna. The most evident temporal variations were for pH, SOC, global enzymatic activity, and feeding activity of the soil fauna. The Cs and Co orchards showed greater richness and abundance of herbaceous species. Organic management favors a timely coverage of multiple benefits, with the presence of the Commoliaceae and Fabaceae families, and offering an ecological effect and green manure of high ecosystem value. In conclusion, agroforestry and biodynamic management systems are the best options to maintain soil quality and functioning for citrus production.