Agroforestry systems bring together social, economic, and environmental services and can be alternatives for promoting development and sustainability in peasant agriculture. This study aimed to evaluate the soil physical and microbiological quality in a four-years peasant agroecological agroforestry intercropped with vegetables, located in Lapa, South Brazil. Treatments included an agroforestry row (AFS-R) managed under no-tillage and cultivated with trees for fruit and wood production; an agroforestry inter-row (AFS-I) managed with conventional tillage and cultivated with vegetables; and an area managed with conventional tillage (CT) for one year and cultivated with landrace maize. Soil physical assessments comprised soil bulk density, total porosity, macroporosity, microporosity, bioporosity, mean weight diameter of aggregates, field capacity, aeration capacity, soil saturated hydraulic conductivity, and the visual evaluation of soil structure. Microbiological indicators included soil microbial biomass, basal respiration, microbial quotient, metabolic quotient, soil organic carbon, and the most probable number of nitrogen-fixing, ammonifying, and nitrite-oxidizing bacteria. The results demonstrated that AFS-R management improved several soil physical and microbiological attributes, highlighting the importance of plants diversity, organic residues input, and no-tillage for soil quality. On the other hand, the tillage practice contributed to structural and microbiological degradation in CT, and more intensively in AFS-I, indicating that more conservationist soil management, like minimum or no-tillage, might be studied as an alternative for the cultivation of vegetable crops in agroforestry systems.