In blue carbon ecosystems, biomarkers and indicators have been developed to assess soil biogeochemical processes and history. In this study, we investigate blue carbon soils to determine if geochemical characteristics can predict soil microbial characteristics, and secondly to investigate if these two indicators can reveal novel information about processes about soil formation and alteration. First, phospholipid fatty acids (PLFAs) identified soil microbial functional groups and abundances. Microbes varied strongly among the three blue carbon ecosystems – seagrass, mangrove and saltmarsh – and to a lesser extent with soil age/depth. Then, x-ray fluorescence using a core scanner (ITRAX) was used to identify geochemical traits of the soil. Lastly, statistical procedures were carried out to test the ability of ITRAX-derived geochemical characteristics to explain the variation in PLFA composition. The soil geochemical indicators for organic matter (OM) source and turnover explained most of the variability in PLFAs, followed by indicators for redox and grain size. For both indicators the saltmarsh soils were associated with relatively higher OM availability and reactivity and microbial abundance. High OM samples also supported a range of microbial functional groups, including fungi and the co-existence of prokaryotic aerobic and anaerobic metabolisms. In contrast, increased depths representing older soil ages showed decreases in OM reactivity and shifts in OM processing through reduced active microbial abundance. We suggest that x-ray fluorescence data used as an indicator in conjunction with other biomarkers can be used to assess multiple aspects of blue carbon soils (biology, provenance, physicochemistry), while also possessing opportunity for future development as rapid field technique.