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The fate of carbon (C) in organisms, food webs, and ecosystems is to a major extent regulated by mass-balance principles and the availability of other key nutrient elements. In relative terms, nutrient limitation implies excess C, yet the fate of this C may be quite different in autotrophs and heterotrophs. For autotrophs nutrient limitation means less fixation of inorganic C or excretion of organic C, while for heterotrophs nutrient limitation means that more of ingested C will “go to waste” in the form of egestion or respiration. There is in general a mismatch between autotrophs and decomposers that have flexible but generally high C:element ratios, and consumers that have lower C:element ratios and tighter stoichiometric regulation. Thus, C-use efficiency in food webs may be governed by the element ratios in autotroph biomass and tend to increase when C:element ratios in food approach those of consumers. This tendency has a strong bearing on the sequestration of C in ecosystems, since more C will be diverted to detritus entering soils or sediments when C-use efficiency is low due to stoichiometric imbalance. There will be a strong evolutionary pressure to utilize such excess C for structural and metabolic purposes. This article explores how these basic principles may regulate C sequestration on different scales in aquatic and terrestrial ecosystems.