Tree-based intercropping (TBI) systems, consisting of a medium to fast-growing woody species planted in widely-spaced rows with crops cultivated between tree rows, are a potential sink for atmospheric carbon dioxide (CO2
). TBI systems contribute to farm income in the long-term by improving soil quality, as indicated by soil carbon (C) storage, generating profits from crop plus tree production and potentially through C credit trading. The objectives of the current study were: (1) to evaluate soil C and nitrogen (N) stocks in soil depth increments in the 0–30 cm layer between tree rows of nine-year old hybrid poplar-hay intercropping systems, to compare these to C and N stocks in adjacent agricultural systems; and (2) to determine how hay yield, litterfall and percent total light transmittance (PTLT) were related to soil C and N stocks between tree rows and in adjacent agricultural systems. The two TBI study sites (St. Edouard and St. Paulin) had a hay intercrop with alternating rows of hybrid poplar clones and hardwoods and included an adjacent agricultural system with no trees (i
., the control plots). Soil C and N stocks were greater in the 0–5 cm depth increment of the TBI system within 1 m of the hardwood row, to the west of the poplar row, compared to the sampling point 1 m east of poplar at St. Edouard (p
= 0.02). However, the agricultural system stored more soil C than the nine-year old TBI system in the 20–30 cm and 0–30 cm depth increments. Accumulation of soil C in the 20–30 cm depth increment could be due to tillage-induced burial of non-harvested crop residues at the bottom of the plow-pan. Soil C and N stocks were similar at all depth increments in TBI and agricultural systems at St. Paulin. Soil C and N stocks were not related to hay yield, litterfall and PTLT at St. Paulin, but hay yield and PTLT were significantly correlated (R
= 0.87, p
< 0.05, n
= 21), with lower hay yield in proximity to trees in the TBI system and similar hay yields in the middle of alleys as in the agricultural system. Nine years of TBI practices did not produce significant gains in soil C and N stocks in the 0–30 cm layer, indicating that the total C budget, including C sequestered in trees and unharvested components (litterfall and roots), must be assessed to determine the long-term profitability of TBI systems in Canada.