The carbon-use-efficiency (CUE) of microorganisms is an important parameter in determining ecosystem-level carbon (C) cycling; however, little is known about how variance in resources affects microbial CUE. To elucidate how resource quantity and resource stoichiometry affect microbial CUE, we cultured four microorganisms - two fungi (Aspergillus nidulans and Trichoderma harzianum) and two bacteria (Pectobacterium carotovorum and Verrucomicrobium spinosum) - under 12 unique C, nitrogen (N) and phosphorus (P) ratios. Whereas the CUE of A. nidulans was strongly affected by C, bacterial CUE was more strongly affected by mineral nutrients (N and P). Specifically, CUE in P. carotovorum was positively correlated with P, while CUE of V. spinosum primarily depended on N. This resulted in a positive relationship between fungal CUE and resource C : nutrient stoichiometry and a negative relationship between bacterial CUE and resource C : nutrient stoichiometry. The difference in the direction of the relationship between CUE and C : nutrient for fungi vs. bacteria was consistent with differences in biomass stoichiometry and suggested that fungi have a higher C demand than bacteria. These results suggest that the links between biomass stoichiometry, resource demand and CUE may provide a mechanism for commonly observed temporal and spatial patterns in microbial community structure and function in natural habitats.