To meet international greenhouse gas reporting obligations, New Zealand must report on carbon stocks in forests established after 1989 (post-1989 forest). Although predominately comprised of planted forest, post-1989 forest also contains a component of natural vegetation amounting to less than 10% by area. New Zealand undertook a national inventory of this natural stratum of post-1989 forest to provide estimates of carbon stocks and stock change in woody species over the first commitment period (2008–2012) of the Kyoto Protocol. Plots were installed on a 4-km grid, and the basal diameters and heights of trees and shrubs were measured for the first time from November 2012, to March 2013. Carbon stocks in 2012 were calculated using allometric functions developed from biomass samples from each site. Basal disc samples provided data on diameter increment and shrub and tree age annually from 1990 to 2012. These were used to predict carbon stocks per ha for individual plots in 2008 and to provide annual predictions by pool back to 1990. Carbon stocks summed across live and dead biomass pools (excluding soil) averaged 3.04, 16.70 and 28.73 t C/ha in 1990, 2008 and 2012, respectively. The disposition by pool was 2.25, 12.54 and 21.84 t C/ha in aboveground biomass, 0.56, 3.13 and 5.46 t C/ha in belowground biomass (using a root/shoot ratio of 0.25), 0.03, 0.17 and 0.23 t C/ha in deadwood, and 0.18, 0.86 and 1.21 t C/ha in litter in 1990, 2008 and 2012, respectively. In 1990, the woody biomass stock estimate per plot ranged from zero to 40 t C/ha and averaged 3.04 t C/ha across all plots. The methodology used to predict annual carbon stocks required an assumption concerning stem annual mortality. Sensitivity analysis suggested that varying this assumption had only a minor impact on predicted carbon stocks and changes. Plant age varied markedly within and between the natural forest plots, and therefore, the mean age of woody vegetation at each site was obtained by setting a threshold woody biomass carbon stock that needed to be achieved, and vegetation age was calculated as years since the threshold was achieved. This threshold approach facilitated the development of a yield table for predicting carbon (t/ha) as a function of vegetation mean age.