Southwestern ponderosa pine forests were dramatically altered by fire regime disruption that accompanied Euro-American settlement in the 1800s. Major changes include increased tree density, diminished herbaceous cover, and a shift from a frequent low-intensity fire regime to a stand-replacing fire regime. Ecological restoration via thinning and prescribed burning is being widely applied to return forests to the pre-settlement condition, but the effects of restoration on ecosystem function are unknown. We measured carbon (C), nitrogen (N), and phosphorus (P) fluxes during the first two years after the implementation of a replicated field experiment comparing thinning and composite (thinning, forest floor fuel reduction, and prescribed burning) restoration treatments to untreated controls in a ponderosa pine forest in northern Arizona, USA. Total net primary productivity (260 g C·m−2·yr−1) was similar among treatments because a 30–50% decrease in pine foliage and fine-root production in restored ecosystems was balanced by greater wood, coarse root, and herbaceous production. Herbaceous plants accounted for <20% of total plant C, N, and P uptake in the controls but from 25% to 70% in restored plots. Total plant N uptake was ∼3 g N·m−2·yr−1 in all treatments, but net N mineralization was just one-half and two-thirds of this value in the control and composite restoration, respectively. Element flux rates in controls generally declined more in a drought year than rates in restoration treatments. In this ponderosa pine forest, ecological restoration that emulated pre-settlement stand structure and fire characteristics had a small effect on plant C, N, and P fluxes at the whole ecosystem level because lower pine foliage and fine-root fluxes in treated plots (compared to controls) were approximately balanced by higher fluxes in wood and herbaceous plants.