•SOC stocks decreased by 12.4% in Costa Rica and 0.13% in Nicaragua after establishment of coffee AFS.•SOC stocks increased in the top 10 cm of soil; greater reduction occurred at 20–40 cm.•Organic management caused a greater increase in 0–10 cm SOC but did not influence reduction at depth.•Shade type effects on SOC were smaller; no significant difference between shaded and unshaded coffee.•SOC stocks tend to converge on a level determined by site environment during establishment.
SOC stocks
decreased
12.4%
%
SOC stocks
decreased
0.13%
%
soil
top 10 cm
cm
soil
20–40 cm
cm
soil
0–10 cm
cm