Using soil organic carbon (SOC) to generate carbon offsets requires reliably quantifying SOC sequestration. However, accuracy of SOC measurement is limited by inherent spatial heterogeneity, variability of laboratory assays, unmet statistical assumptions, and the relatively small magnitude of SOC changes over time, among other things. Most SOC measurement protocols currently used to generate offsets for C markets do not adequately address these issues, threatening to undermine climate change mitigation efforts. Using analyses and simulations from 1,117 soil samples collected from California crop and rangelands, we quantified measurement errors and sources of uncertainty to optimize SOC measurement. We demonstrate that (1) spatial heterogeneity is a primary driver of uncertainty; (2) dry combustion assays contribute little to uncertainty, although inorganic C can increase error; (3) common statistical methods—Student’s t-test and its relatives—can be unreliable for SOC (e.g. at low to medium sample sizes or when the distribution of SOC is skewed), which can lead to incorrect interpretations of SOC sequestration; and (4) common sample sizes (10–30 cores) are insufficiently powered to detect the modest SOC changes expected from management in heterogeneous agricultural landscapes. To reduce error and improve the reliability of future SOC offsets, protocols should: (1) require power analyses that include spatial heterogeneity to determine minimum sample sizes, rather than allowing arbitrarily small sample sizes; (2) minimize the use of compositing; (3) require dry combustion analysis, by the same lab for all assays; and (4) use nonparametric statistical tests and confidence intervals to control Type I error rates. While these changes might increase costs, they will make SOC estimates more accurate and more reliable, adding credibility to soil management as a climate change mitigation strategy.