The molecular composition of soil organic carbon remains contentious. Microbial-, plant-, and fire-derived compounds may each contribute, but do they vary predictably among ecosystems? Here we present carbon functional groups and molecules from a diverse spectrum of North American surface mineral soils, primarily collected from the National Ecological Observatory Network, quantified by nuclear magnetic resonance spectroscopy and a molecular mixing model. Soils varied widely in relative contributions of carbohydrate, lipid, protein, lignin, and char-like carbon, but each compound class had similar overall abundance. Three principal component axes explained 90% of the variance in carbon composition: the first showed a tradeoff between lignin and protein, the second showed a tradeoff between carbohydrate and char, and the third was explained by lipids. Reactive aluminum, crystalline iron oxides, and pH plus overlying organic horizon thickness best explained variation along each respective axis; these predictors were ultimately related to climate. Together, our data point to continental-scale tradeoffs in soil carbon molecular composition which are linked to environmental and geochemical variables known to predict carbon mass concentrations. Controversies regarding the genesis of soil carbon and its potential responses to global change can be partially reconciled by considering diverse ecosystem properties that drive complementary persistence mechanisms.