The production of vegetables and grains by the family farming in the mountains of the Atlantic Forest is characterized by intensive soil management with ploughing and harrowing practices. These practices are promoting hydric erosion and losses of soil quality in the region. In this context, the objective of this work was to evaluate soil physical and biological characteristics at two seasons of the year in agroecosystems producing vegetables and grains in the no-tillage system (NTS) for 3, 5, and 9 years compared to the conventional management system (CT) in the Atlantic Forest Biome, Brazil. Physical and organic matter attributes and carbon (C) and nitrogen (N) stock were evaluated. NTS showed, in general, greater total porosity than CT systems. The main differences between the systems were found in the organic attributes and C and N stocks. The content of microbial biomass C in NTS with 3, 5, and 9 years was 767.5, 326.5, and 210.0 mg·kg−1, while the areas with CT had 93.75, 78.25, and 45.75 mg·kg−1, respectively. The stock of C in winter at the 9NTS area was 33.0 and 41.5 Mg·ha−1, and the respective area in CT presented only 21.75 and 25.00 Mg·ha−1 in the depths of 0–10 and 10–20 cm, respectively. The metabolic quotient of the NTS areas did not differ from the reference ecosystems and is promoting lower C-CO2 emissions than the CT system. The adoption of NTS in vegetable production improves soil quality in family farm areas of mountains relief at the Atlantic Forest Biome.