Forests are major carbon (C) sinks, but their ability to sequester C and thus mitigate climate change, varies with the environment, disturbance regime, and biotic interactions. Herbivory by invasive, nonnative ungulates can have profound ecosystem effects, yet its consequences for forest C stocks remain poorly understood. We determined the impact of invasive ungulates on C pools, both above-and belowground (to 30 cm), and on forest structure and diversity using 26 paired long-term (>20 years) ungulate exclosures and adjacent unfenced control plots located in native temperate rainforests across New Zealand, spanning 36-41 S. Total ecosystem C was similar between ungulate exclosure (299.93 ± 25.94 Mg C ha −1 ) and unfenced control (324.60 ± 38.39 Mg C ha −1 ) plots. Most (60%) variation in total ecosystem C was explained by the biomass of the largest tree (mean diameter at breast height [dbh]: 88 cm) within each plot.Ungulate exclusion increased the abundance and diversity of saplings and small trees (dbh ≥2.5, <10 cm) compared with unfenced controls, but these accounted for ~5% of total ecosystem C, demonstrating that a few, large trees dominate the total forest ecosystem C but are unaffected by invasive ungulates at a timescale of 20-50 years. However, changes in understory C pools, species composition, and functional diversity did occur following long-term ungulate exclusion. Our findings suggest that, although the removal of invasive herbivores may not affect total forest C at the decadal scale, major shifts in the diversity and composition of regenerating species will have longer term consequences for ecosystem processes and forest C. K E Y W O R D S biological invasion, carbon cycle, climate change mitigation, exclosure treatment, forest ecosystem processes, functional dispersion, large herbivore effects in forests, long-term permanent plot network, nonnative species' impacts, plant population responses