Tropospheric ozone (O3) effectively deposits to forested ecosystems but the fate of O3 within the forest canopy is unresolved. We partitioned total measured ecosystem daytime O3 deposition to a ponderosa pine (Pinus ponderosa) forest into its major loss pathways; stomatal uptake, non-stomatal surface deposition, and gas-phase chemistry. Total O3 flux was dominated by gas-phase chemistry during the summer and by stomatal uptake during winter. O3 loss due to gas-phase chemistry was exponentially dependent on temperature, with the same functionality as biogenic hydrocarbon emissions, implicating reactions with biogenic hydrocarbons as the likely gas-phase chemical O3 loss process within the canopy. The reaction of O3 with biogenically-emitted hydrocarbons leads to both hydroxyl radical formation and secondary aerosol growth with important effects on atmospheric chemistry and climate.