In the UK and other temperate regions, short rotation coppice (SRC) and Miscanthus x giganteus (Miscanthus) are two of the leading ‘second-generation’ bioenergy crops. Grown specifically as a low-carbon (C) fossil fuel replacement, calculations of the climate mitigation provided by these bioenergy crops rely on accurate data. There are concerns that uncertainty about impacts on soil C stocks of transitions from current agricultural land use to these bioenergy crops could lead to either an under- or overestimate of their climate mitigation potential. Here, for locations across mainland Great Britain (GB), a paired-site approach and a combination of 30-cm- and 1-m-deep soil sampling were used to quantify impacts of bioenergy land-use transitions on soil C stocks in 41 commercial land-use transitions; 12 arable to SRC, 9 grasslands to SRC, 11 arable to Miscanthus and 9 grasslands to Miscanthus. Mean soil C stocks were lower under both bioenergy crops than under the grassland controls but only significant at 0–30 cm. Mean soil C stocks at 0–30 cm were 33.55 ± 7.52 Mg C ha−1 and 26.83 ± 8.08 Mg C ha−1 lower under SRC (P = 0.004) and Miscanthus plantations (P = 0.001), respectively. Differences between bioenergy crops and arable controls were not significant in either the 30-cm or 1-m soil cores and smaller than for transitions from grassland. No correlation was detected between change in soil C stock and bioenergy crop age (time since establishment) or soil texture. Change in soil C stock was, however, negatively correlated with the soil C stock in the original land use. We suggest, therefore, that selection of sites for bioenergy crop establishment with lower soil C stocks, most often under arable land use, is the most likely to result in increased soil C stocks.