To determine the rates of increase in C and N stocks in the soil and organic layers following afforestation in Andisols, we measured C and N densities in the organic and soil layers at depths of 0–5, 5–15 and 15–30 cm, together with a chronosequence analysis of 4-year-old, 14-year-old and 23-year-old Japanese cedar (Cryptomeria japonica) and 4-year-old, 12-year-old and 25-year-old Hinoki cypress (Chamaecyparis obtusa) plantations. The short-term changes in C and N were confirmed by repeated sampling 5 years after the first sampling. Tree growth, biomass accumulation and organic layers were much greater in Japanese cedar than in Hinoki cypress plantations. Soil C density (kg m−3) increased and bulk density decreased with stand age in the surface layer (0–5 cm). The average soil C accumulation rate was 22.9 g C m−2 year−1 for Japanese cedar and 21.1 g C m−2 year−1 for Hinoki cypress. Repeated sampling showed that the rate of increase in C in the surface soil was relatively slow in young stands and that soil C density (kg m−3) in the subsurface soil did not change over a 5-year period. Although N accumulated in the tree biomass and organic layers, the soil N density (kg m−3) did not change after afforestation. Although the andic properties of the soil and differences in the planted species did not influence the rate of increase in soil C, soil C density was expected to increase to a concentration greater than 80 g kg−1, possibly because of the large C accumulation capacity of Andisols.