Quantifying and understanding the small-scale variability of nitrous oxide (N₂O) and carbon dioxide (CO₂) emission are essential for reporting accurate ecosystem greenhouse gas budgets. The objective of this study was to evaluate the spatial pattern of soil CO₂ and N₂O emissions and their relation to topography in a tropical montane forest. We measured fluxes of N₂O and CO₂ 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 N₂O and CO₂ fluxes at the plot level. Topography exhibited a major influence on N₂O emissions, with soils at midslope position emitting significantly less than at ridgetops and valley bottoms, but no consistent effect of topography on soil CO₂ emissions was found. The high spatial variation of N₂O and CO₂ fluxes was further increased by changes in vegetation and soil properties resulting from human disturbance associated with charcoal production. Soil N₂O and CO₂ fluxes showed no spatial pattern at the plot level, with “hot spots” strongly contribu ... mehrting to the total emissions (10% of the soil cores represented 73 and 50% of the total N₂O and CO₂ emissions, respectively). Thus, a large number of samples are needed to obtain robust estimates of N₂O and CO₂ 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 CO₂ and N₂O fluxes at the ecosystem scale.