Increasing the carbon (C) content of agricultural soils can help mitigate rising atmospheric CO2 concentrations, improve soil health and increase crop yield. Unlike annual cropping systems, soils planted to perennial woody crops, such as vineyards and orchards, are left undisturbed for many years making them particularly amenable to soil C storage. Here, we used a regional sampling campaign of over 80 commercially-managed sites across the Okanagan Valley, in the southern interior of British Columbia, Canada, to examine the spatial distribution of soil C under irrigated perennial woody crops. Using this living lab approach, we collected soils from the crop and drive rows of apple and cherry orchards, and vineyards subjected to a wide range of real-life management regimes (e.g., for weed and pest control, fertilizer application, etc.). Sites were selected with soils belonging to five surficial deposit classes, representing 40% of the mapped agricultural land area. Soil C was spatially heterogeneous across all the sites, with the surface soil (0–15 cm) of drive rows containing more C than the soil in adjacent crop rows. Clear differences emerged among cropping systems, despite the variation in management practices applied by individual growers. Drip-irrigated apple orchards showed the greatest spatial heterogeneity, with C concentrations of 2.9% in the drive row and 1.8% in the crop row, while vineyard and cherry orchard soils showed the least, with differences between crop and drive rows of approximately 0.3%. Higher C concentrations in the drive rows appeared to be the result of recently assimilated/less processed litter and fine root C inputs from the shallow-rooted understory vegetation. This was confirmed using stable isotope analysis: drive row soil C was significantly 13C depleted compared to the crop row soil, to a depth of 30 cm. Overall, cherry orchards contained the most C (70 Mg C ha−1 to a depth of 30 cm), vineyards the least (48 Mg C ha−1), and apple orchards were intermediate (66 Mg C ha−1). A recent land-use survey in 2015 determined that 8501 ha of agricultural land in the Okanagan Valley was planted to apples, cherries or grapes, and that large shifts in crop land area have occurred since the previous survey, conducted in 2006. We estimate that apple orchards currently hold approximately 199 Gg C, vineyards 188 Gg C and cherry orchards 110 Gg C. Marked differences in soil C storage between the cropping systems, despite the fact some were less than 10 years old, suggests that soils in this region are responsive to changes in crop and associated management practices over relatively short time periods. We conclude that the drive rows of vineyards offer the greatest scope for increased soil C storage among woody perennial horticultural cropping systems in the Okanagan Valley but that ‘long-term’ soil carbon storage may not be possible in these soils.