Anthropogenic activities are increasing the concentration of atmospheric CO₂.  Some studies have reported an increase in nitrogen (N) fixation in systems exposed to elevated CO₂, a response that would alleviate nutrient limitations to soil carbon storage. We report that N fixation and soil organic matter decline after long-term exposure to elevated CO₂ in a Florida scrub-oak ecosystem.  Increases in above-ground biomass may bind metal nutrients in forms unavailable to N fixing microbes and their plant symbionts, and constrain fixation and carbon storage.  The most important of these nutrients for N fixation is molybdenum (Mo), a requisite cofactor of nitrogenase.  Mo availability is also limited by the presence of oxides of iron, aluminum and manganese in soil.  No study to date has examined the influence of elevated CO₂ on these metal oxides and their impact on Mo availability.  We present data suggesting that the decline in N fixation in the scrub-oak ecosystem is due to significantly lower Mo concentrations in symbiotic nitrogen fixing plants exposed to elevated CO₂, which may be related to our observed differences in stand level oak [Mo].  We have also observed significant differences in the concentration of soil organic matter and metal oxides between the CO₂ treatments and suggest that interactions between soil metal nutrients, their response to elevated CO₂ and their impact on N fixation is critical to understand ecosystem response to elevated CO₂.