Abstract Background Soils are important global carbon pools that are under threat from intensive land use through a variety of agricultural practices. Sustainable management of agricultural soils may have the potential to mitigate climate change through increased carbon sequestration and increase their fertility. Among management practices to increase carbon sequestration, crop rotation designs have often been tested on yield effects in long-term agricultural experiments. However, in these studies, soil organic carbon (SOC) was monitored but not always the key objective. Thus, here we provide a method for a systematic review to test the effects of common crop rotations on SOC sequestration to provide evidence on the most sustainable management regimes that can promote SOC storage. Methods This systematic review incorporates studies concerning selected crop rotations (rotations-vs-monocultures, legumes-vs-no legumes, and perennials-vs-annuals) collated in a recently completed systematic map on the effect of agricultural management on SOC, restricted to boreo-temperate systems (i.e., the warm temperate climate zone). Some 208 studies relevant for this systematic review were identified in the systematic map. An update of the original search (September 2013) will be undertaken to identify newly published academic and grey literature. Studies will be critically appraised for their internal and external validity, followed by full data extraction (meta-data describing study settings and quantitative study results). Where possible, studies will be included in meta-analyses examining the effects of the different rotational practices. Implications of the findings will be discussed in terms of policy, practice and research, and the nature of the evidence base.