Use of soil cover crops of different families in crop rotation or succession under no-tillage system (NTS) for onion production results in higher soil quality compared to land use systems with less plant diversity. The objective was to evaluate the effect of using different combinations of plant species from different botanical families in rotation and succession of soil cover crops in NTS for onion production on formation of macroaggregates, mesoaggregates, and microaggregates, and on total organic C (TOC) and N (TN) contents, including isotopic forms of C and N, in soil aggregates and bulk soil. The treatments (T) evaluated were maize/onion (NTS-T1); cover plants (winter)/onion (NTS-T2); maize/winter grasses/onion (NTS-T3); velvet bean/onion (NTS-T4); millet/cover plants (winter)/onion (NTS-T5); velvet bean/rye/onion (NTS-T6); maize/onion in conventional tillage system (CTS-T7); and intercrop cover plants (summer)/onion (NTS-T8). We evaluated macroaggregates (8.0–0.25 mm), microaggregates (<0.25 mm), and bulk soil (<2.0 mm) at depths of 0–5, 5–10, and 10–20 cm, in a nine-year field experiment. The greater plant diversity in T2–T6 and T8 resulted in higher geometric mean diameter (GMD) of aggregates compared to T1 and T7. The T8 was more efficient in increasing GMD in the 10–20 cm soil depth than the other treatments. The T1 was more efficient in improving the evaluated soil physical and chemical attributes than T7. The use of NTS with plants of the Poaceae and Fabaceae families in single or intercrop systems for onion production resulted in higher TOC and TN contents in the 0–5 and 5–10 cm soil depths compared to CTS. Isotope 15N measurements showed that C and N were more protected in microaggregates in all evaluated treatments and depths compared to macroaggregates and bulk soil. Macroaggregates had more TOC and TN than microaggregates.