Intraspecific variation in response to rising atmospheric carbon dioxide concentration [CO2] could be used as a means to begin selection for improved quantitative or qualitative characteristics for a given crop. Peanut (Arachis hypogaea L.) is a leguminous crop of global importance; however multiyear field assessments of intraspecific variation in yield or seed quality in regard to rising atmospheric [CO2] are scarce. In the current study, we examined the seed yield, above-ground biomass, and concentration of a seed storage protein and primary allergen (Ara h 1) for two peanut cultivars with distinct morphologies, ‘Virginia Jumbo’ and ‘Georgia Green’, grown in open-top field chambers at ambient or ambient + 250 µmol mol−1 [CO2] for a 2-yr period. Significant differences in cultivar, [CO2], and cultivar × [CO2] were observed for above-ground biomass and seed (peanut) yield, with Virginia Jumbo showing a consistently greater increase relative to Georgia Green in response to elevated [CO2]. The greater quantitative response of Virginia Jumbo to [CO2] was also concurrent with a significant increase in the concentration of Ara h 1 for this cultivar, which, in turn, was negatively correlated with overall protein concentration. While preliminary, these results indicate that selection opportunities exist to match yield increases to rising [CO2] for peanut through genetic or phenotypic selection; in addition, these are also the first data to show that [CO2]-induced qualitative changes, particularly in regard to increased allergen concentration, should also be considered to address food safety concerns.