Abstract Quantifying and understanding the small‐scale variability of nitrous oxide (N 2 O) and carbon dioxide (CO 2 ) emission are essential for reporting accurate ecosystem greenhouse gas budgets. The objective of this study was to evaluate the spatial pattern of soil CO 2 and N 2 O emissions and their relation to topography in a tropical montane forest. We measured fluxes of N 2 O and CO 2 from 810 sampling locations across valley bottom, midslope, and ridgetop positions under controlled laboratory conditions. We further calculated the minimum number of samples necessary to provide best estimates of soil N 2 O and CO 2 fluxes at the plot level. Topography exhibited a major influence on N 2 O emissions, with soils at midslope position emitting significantly less than at ridgetops and valley bottoms, but no consistent effect of topography on soil CO 2 emissions was found. The high spatial variation of N 2 O and CO 2 fluxes was further increased by changes in vegetation and soil properties resulting from human disturbance associated with charcoal production. Soil N 2 O and CO 2 fluxes showed no spatial pattern at the plot level, with “hot spots” strongly contributing to the total emissions (10% of the soil cores represented 73 and 50% of the total N 2 O and CO 2 emissions, respectively). Thus, a large number of samples are needed to obtain robust estimates of N 2 O and CO 2 fluxes. Our results highlight the complex biogeochemical cycling in tropical montane forests, and the need to carefully address it in research experiments to robustly estimate soil CO 2 and N 2 O fluxes at the ecosystem scale.