Subsurface carbon stocks are a prime target for efforts to increase soil carbon storage for climate change mitigation and improving soil health. However, subsurface carbon (C) dynamics are not well understood, especially in soils under long term intensive agricultural management. We compared subsurface C dynamics in tomato-corn rotations after 25 years of differing C and nutrient management in the California Central Valley: CONV (mineral fertilizer), CONV+WCC (mineral fertilizer + cover crops) and ORG (composted poultry manure + cover crops). Our results showed a ~19 Mg/ha increase in SOC stocks down to 1 m under ORG systems, no significant SOC increases under CONV+WCC or CONV systems, and the accumulation of carboxyl rich C in the subsurface (60–100 cm) horizons of all systems. Systems also had greater amounts of aromatic carbon in the order ORG>CONV+WCC>CONV. We identified a potential interaction between cover crops and compost, theorizing that increased macropores from cover crop roots facilitate the transport of soluble C and nutrients into the subsurface, thereby increasing stocks. These results demonstrate the potential for subsurface carbon storage in tilled agricultural systems and highlight a potential pathway for increasing carbon transport and storage in subsurface soil layers.