The use of rock powders is an agricultural practice that facilitates the agroecological transition and autonomy of many farmers. These inputs should be used in conjunction with management systems that enhance the weathering of the minerals contained in the rocks. This study aimed to assess the impact of incorporating gneiss powder on soil quality and coffee cultivation within agroecological and organic frameworks, encompassing agroforestry systems (AFSs) as well as areas fully exposed to sunlight (FS). Comprehensive analyses, including chemical, microbiological, and physical assessments, were carried out on the soil. The study involved evaluating various parameters such as electrical conductivity, grain density, total titratable acidity, and pH of the exudates to gauge the coffee quality. Following a 24-month application of rock powder, noteworthy observations included increased soil moisture in agroforestry systems (AFSs), presumably attributable to enhanced nutrient availability (potassium, calcium, magnesium, copper, and zinc) derived from the gneiss powder. In addition, a higher level of CO2 was derived from microbial respiration than from soil production. Similarly, coffee beans presented lower electrical conductivity, higher density, and fewer defects in AFSs than fully exposed sun systems (FS). The total titratable acidity values remain consistent with the limits indicated in the literature for quality coffees; the pH values, however, were lower. The results suggest that the use of gneiss powder enhances soil microorganism activity and accelerates the biological weathering of minerals for coffee plantations in AFSs.