Onion (Allium cepa L.) is a food crop of economic importance. In Brazil, the crop typically occurs in a conventional tillage system (CT), which favors the mineralization and decomposition of soil organic matter (SOM) and the loss of carbon (C) and nitrogen (N). On the other hand, the no-tillage vegetable system (NTVS) operates based on sustainable pillars and bypasses the adverse effects of CT. This study evaluated the total C and N stocks and particle-size fractions of SOM in NTVS with single and intercropped cover plants compared to vegetable crops under CT. The NTVS evaluated treatments were as follows: (1) spontaneous vegetation (SV); (2) black oats (BO); (3) rye (RY); (4) oilseed radish (OR); (5) RY + OR; and (6) BO + OR. A treatment under CT with millet cover, a no-tillage system with (NTS) millet + velvet + sunflower cover, and a forested area as the original condition was also evaluated. Soil samples were collected in 0–5, 5–10, and 10–30 cm layers. Stocks of total organic C (TOC), total N (TN), particulate OC (POC), particulate N (PN), mineral-associated OC (MAOC), and mineral-associated N (MN) were evaluated. The highest stocks of TOC, TN, POC, and NM were found in NTVS compared to CT, and RY + OR showed the best results. The NTVS showed higher TOC and TN stocks with grasses and cruciferous intercropped than NTVS with SV and CT. POC and PN stocks increased in areas with single and intercropped RY and OR treatments. MAOC and MN stocks were higher than forest in RY + OR intercrop in the topsoil layer. RY and OR intercrop efficiently added C and N to the soil under NTVS. The consortium of millet + velvet + sunflower in NTS showed higher TOC, TN, POC, and PN stocks compared to the other treatments (0–5 and 0–30 cm). In general, the intercrop of cover plants is ideal for obtaining the NTVS maximum potential, favoring several mechanisms between soil, plant, and atmosphere, resulting in improved soil quality, increased organic matter, and higher stocks of C and N.