The dataset includes monthly and annual soil CO2, N2O and CH4 fluxes, and their soil controlling factors measured at two forests that had undergone conventional selective logging and reduced-impact logging in Cameroon. Each logging system had four replicate plots and each plot included the disturbed strata (road, logging deck, skidding trail, and felling gap) and an undisturbed reference area. Measurements were conducted monthly over one year. Annual fluxes are estimated based on trapezoidal rule between measured fluxes and sampling day intervals, assuming constant flux rates per day.