Cover cropping is a promising management practice for soil health and climate change mitigation by improving soil organic carbon (SOC) and total nitrogen (TN) stocks. However, limited studies focused on deeper soil layers (>30 cm depth) where soil C is more stable than that in surface soil (≤30 cm depth). Here, deep soil sampling was conducted in a 15-year cover cropping experiment, in a horticulture-grain system on sandy loam soil. The SOC and TN stocks were expressed on an equivalent soil mass basis using a cubic spline model. Overall, long-term cover cropping had significantly greater SOC and TN stocks by 22 % (95 %CI: 5–43 %) and 26 % (95 %CI: 6–49 %), respectively in the 0–120 cm depth, compared to no cover cropping. Additionally, the mean SOC and TN sequestration rate (0–30 cm depth) was 0.53 Mg C ha−1 yr−1 and 0.06 Mg N ha−1 yr−1, respectively. However, if only 0–15 cm depth was evaluated, long-term cover cropping did not significantly affect SOC and TN stocks. These results indicated that shallow sampling (<15 cm depth) may not provide comprehensive information on the effect of long-term cover cropping on soil C and N storage. To better understand the mechanism of bulk soil C and N storage, we investigated their distribution between particulate and mineral-associated organic matter pools (POM and MAOM). We found POM pool was the main store of bulk SOC and TN stocks in surface soils while it was the MAOM pool in deeper soil layers, without soil texture change with soil depth. These findings indicated that soil C and N sources for bulk SOC and TN accrual differed in surface and deeper soils. Our study demonstrated that long-term cover cropping can facilitate SOC accumulation in the soil below 15 cm deep, which calls into question carbon capture protocols that focus on shallow soil depths.