The choice of the type of background spectrum affects the credibility of open-path Fourier transform infrared spectroscopy (OP/FT-IR) data, and consequently, the quality of data analysis. We systematically investigated several properties of the background spectrum. The results show that a short-path background measured with the lowest amplifier gain could significantly reduce noise in the calculated absorbance spectrum, by at least 30% in our case. We demonstrated that by using a short-path background, data analysis is more resistant to interferences such as wavenumber shift or resolution alteration that occurs as a consequence of aging hardware or misalignment. We discussed a systematic error introduced into quantitative analyses by the short-path background and developed a procedure to correct that error. With this correction approach, a short-path background established five years ago was still found to be valid. By incorporating these findings into the protocol for quantitative analysis, we processed the measurements with two OP/FT-IR instruments set up side by side in the vicinity of a large dairy farm, to monitor NH3, CH4, and N2O. The two sets of calculated concentrations showed high agreement with each other. The findings of our investigations are helpful to atmospheric monitoring practitioners of OP/FT-IR spectroscopy and could also be a reference for future amendments to the protocols outlined in the guidelines of the U.S. Environmental Protection Agency, the American Society for Testing and Materials, and the European Committee for Standardization.