Nature-based solutions (NbS) can address climate change, biodiversity loss, human well-being and their interactions in an integrated way. A major barrier to achieving this is the lack of comprehensiveness in current carbon accounting which has focused on flows rather than stocks of carbon and led to perverse outcomes. We propose a new comprehensive approach to carbon accounting based on the whole carbon cycle, covering both stocks and flows, and linking changes due to human activities with responses in the biosphere and atmosphere. We identify enhancements to accounting, namely; inclusion of all carbon reservoirs, changes in their condition and stability, disaggregated flows, and coverage of all land areas. This comprehensive approach recognises that both carbon stocks (as storage) and carbon flows (as sequestration) contribute to the ecosystem service of global climate regulation. In contrast, current ecosystem services measurement and accounting commonly use only carbon sequestration measured as net flows, while greenhouse gas inventories use flows from sources to sinks. This flow-based accounting has incentivised planting and maintaining young forests with high carbon uptake rates, resulting, perversely, in failing to reveal the greater mitigation benefit from protecting larger, more stable and resilient carbon stocks in natural forests. We demonstrate the benefits of carbon storage and sequestration for climate mitigation, in theory as ecosystem services within an ecosystem accounting framework, and in practice using field data that reveals differences in results between accounting for stocks or flows. Our proposed holistic and comprehensive carbon accounting makes transparent the benefits, trade-offs and shortcomings of NbS actions for climate mitigation and sustainability outcomes. Adopting this approach is imperative for revision of ecosystem accounting systems under the System of Environmental-Economic Accounting and contributing to evidence-based decision-making for international conventions on climate (UNFCCC), biodiversity (CBD) and sustainability (SDGs).