In natural ventilation system-enabled dairy buildings (NVDB), achieving accurate gas emission values is highly complicated. The external weather affects measurements of the gas concentration of pollutants (𝑐𝑃) and volume flow rate (Q) due to the open-sided design. Previous research shows that increasing the number of sensors at the side opening is not cost-effective. However, accurate measurements can be achieved with fewer sensors if an optimal sampling position is identified. Therefore, this study attempted to calibrate the outlet of an NVDB for the direct emission measurement method. Our objective was to investigate the 𝑐𝑃 gradients, in particular, for ammonia (𝑐𝑁𝐻3), carbon dioxide (𝑐𝐶𝑂2), and methane (𝑐𝐶𝐻4) considering the wind speed (v) and their mixing ratios ([cCH4/cNH3]) at the outlet, and assess the effect of sampling height (H). The deviations in each 𝑐𝑃 at six vertical sampling points were recorded using a Fourier-transform infrared (FTIR) spectrometer. Additionally, wind direction and speed were recorded at the gable height (10 m) by an ultrasonic anemometer. The results indicated that, at varied heights, the average 𝑐𝑁𝐻3 (p < 0.001), 𝑐𝐶𝑂2 (p < 0.001), and (p < 0.001) were significantly different and mostly concentrated at the top (H = 2.7). Wind flow speed information revealed drastic deviations in 𝑐𝑃, for example up to +105.1% higher 𝑐𝑁𝐻3 at the top (H = 2.7) compared to the baseline (H = 0.6), especially during low wind speed (v < 3 m s−1) events. Furthermore, [cCH4/cNH3] exhibited significant variation with height, demonstrating instability below 1.5 m, which aligns with the average height of a cow. In conclusion, the average 𝑐𝐶𝑂2, 𝑐𝐶𝐻4, and 𝑐𝑁𝐻3 measured at the barn’s outlet are spatially dispersed vertically which indicates a possibility of systematic error due to the sensor positioning effect. The outcomes of this study will be advantageous to locate a representative gas sampling position when measurements are limited to one constant height, for example using open-path lasers or low-cost devices.