The majority of experiments investigating the population and community level consequences of altered carbon and nitrogen availability implicitly assume a fixed range of ability to obtain and process these nutrients. This may be fair when considering long-lived organisms, however, short-lived organisms (e.g. microbes) will pass through many more generations in the same time period providing scope for evolutionary adaptation. Using isolates of a natural fungal population we demonstrate significant adaptation to carbon-limitation, but not to nitrogen-limitation, over a modest number of generations. However, adaptation comes at a cost: those adapted to carbon-limitation are significantly worse competitors for limited nitrogen when compared with their ancestors. The potential for adaptation (and correlated cost) we demonstrate with our model system highlights the need to consider evolutionary adaptation when interpreting responses of populations, communities and ecosystems to treatments that manipulate, either directly or indirectly, resource availability.