Much of the uncertainty in the biogeochemical behavior of soil carbon (C) in humid tropical ecosystems derives from an incomplete understanding of soil C stabilization processes. Long-term soil C stability is traditionally attributed to organomineral interactions, however, the 2:1 phyllosilicate clays often associated with temperate organomineral complexation are largely absent in humid tropical soils due to extensive weathering. In contrast, these soils contain a spectrum of iron- and aluminum-bearing minerals, exhibiting a broad range of crystallinity, surface area and surface charge, and susceptible to frequent reduction-oxidation (redox) oscillations. This dissertation investigates the composition, distribution, and function of iron-mediated organomineral associations across a range of spatial scales within the Luquillo Critical Zone Observatory (LCZO). Underlain by contrasting lithologies, the LCZO is characterized by highly-weathered, volcaniclastic Oxisols or quartz diorite-derived Inceptisols, producing an experimental gradient of iron content and speciation. To characterize the interactions between inherently heterogeneous soil C and often amorphous mineralogy, this dissertation paired high-resolution analytical techniques and inorganic selective dissolution experiments. We found low-crystallinity, short-range-order (SRO) iron and crystalline iron phases exert control on distinct reservoirs of soil C across both soil types. Notably, organomineral associations were responsible for accumulation of a subset of soil C, rather than driving trends in total soil C. Examination of solid-phase speciation across soil types revealed evidence for unique mineral matrix architecture in each soil. SRO FeIII-oxhydroxide phases in Oxisol soils were also found to be resistant to laboratory reduction events, suggesting that these phases are immune to redox-induced dissolution and may provide a long-term C stabilization mechanism. Investigation of iron-associated C at the molecular scale revealed preferential complexation of distinct C compounds has occurred at mineral interfaces of varying crystallinity and reactivity, suggesting that the array of association mechanisms described may be fractionating soil C. This work demonstrates that iron-mediated organomineral association serves as a reactive filter for soil C across spatial and temporal scales, which may impact both the quantity and identity of C cycling through the critical zone.