AbstractIncorporating large amounts of woody biomass into soil, such as in whole orchard recycling (WOR), can promote carbon sequestration, nutrient recycling, and ecosystem health in agricultural fields. Yet uncertainty regarding the effects of WOR on soil carbon (C) and nitrogen (N) dynamics influences management decisions. The objective of this research was to evaluate the effects of woodchip (WC) size and interaction with N fertilization on carbon dioxide (CO2) and nitrous oxide (N2O) emissions. An 8‐month incubation experiment incorporating WC (4% w/w, equivalent to ∼40 tons per acre) in four sieved sizes (0.2–1.6, 1.6–3.2, 3.2–6.4, and 6.4–12.7 mm) with and without N applications was conducted. All treatments with WC showed that CO2 emission peaked within the first week, then decreased drastically afterward. The CO2 peak delayed as the peak value decreased (WC size increased). The finest WC (<1.6 mm) yielded the lowest total CO2 emissions and resulted in the greatest increase in soil C at the end of incubation. Nitrogen application reduced total CO2 emissions by 1% in the smallest WC size and by 8%–9% for those larger than 1.6 mm. The N2O emissions spiked following each fertilizer application with lowest total emissions from the smallest WC size, suggesting substantial N immobilization. The results imply that larger WC sizes can delay C mineralization and reduce initial N immobilization risks, but the smallest WC size may have stabilized and increased soil organic carbon. This research increased our understanding on WC mineralization that can be used in WOR management.