Blue carbon ecosystems (BCEs), such as mangroves, tidal marshes, and seagrasses, are attracting interest for their potential to mitigate climate change arising from their high rates of carbon accumulation and the significant carbon stocks in their sediments. However, current sediment carbon sampling methods present a mixture of approaches adopted from paleoenvironmental methods focused on historical reconstruction of carbon accumulation, and from soil science methods developed to provide highly accurate and spatially representative carbon stock measurements. Currently, no international standard method for sediment carbon stock analysis exists. Consequently, current estimates of sediment carbon stock values for BCEs may have large uncertainties due to variable methodology. We reviewed and analysed the methods used 217 studies included in two recent global syntheses of carbon stocks in mangrove forest ecosystems to illustrate a lack of consistency in sediment sampling. We then outline how the choice of study design and field sampling methods can introduce inaccuracies and uncertainties in sediment carbon stock analysis. We conclude with examples of how each of these challenges can be resolved and how greater carbon stock quantification accuracy and higher spatial integration can be achieved for blue carbon ecosystems in the future.