Our understanding of the effect of agroforestry systems on soil organic carbon (SOC) is largely limited to the upper layer of the mineral soil, while LFH (litter, partially decomposed litter and humus) and deeper soil layers are poorly studied. In this study, the effects of three different agroforestry systems (hedgerow, shelterbelt, and silvopasture) and their component land-cover types (treed area and adjacent herbland) on SOC stock in LFH and mineral soil layers (0–75 cm) were investigated across 36 sites in central Alberta, Canada. The SOC stock of mineral soil (0–75 cm) was not affected by agroforestry systems but by land-cover type. The treed area had greater (p < 0.001) SOC in the 0–75 cm mineral soil (25.5 kg C m−2) than the herbland (19.4 kg C m−2), driven by the greater (p < 0.001) SOC level in the top 0–30 cm rather than that in the deeper layers (30–75 cm). Within the treed area, the silvopasture system that was dominated by broad-leaf deciduous trees had 56–70% more SOC in the 0–10 cm soil than in the hedgerow and shelterbelt systems. The SOC stock in the 0–10 cm layer was positively (p = 0.025) related to the C stock of the overlying LFH layer in the silvopasture system. These results together with the 22–24% higher dissolved organic carbon (DOC) concentration in the silvopasture than in the other systems suggest that the greater SOC stock in the 0–10 cm mineral soil could be attributed to the higher rates of translocation of DOC from the LFH in the silvopasture than that in shelterbelt or hedgerow. We conclude that SOC stock in the top mineral soil (e.g., 0–30 cm) is more responsive to changes in land-cover type and the LFH layer plays an important role in increasing SOC stock in the surface mineral soil of the agroforestry systems in central Alberta.