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Ammonia (NH3) emissions can negatively affect ecosystems and human health, so they should be monitored and mitigated. This study presents methodology for the estimation of uncertainties in NH3 emissions measurements using the solar occultation flux (SOF) method. The reactive nature of NH3 makes its measurement challenging, but SOF offers a reliable open-path passive method which utilizes solar spectrum data, thereby avoiding gas adsorption within the instrument. To compute NH3 gas fluxes, horizontal and vertical wind speed profiles, as well as plume height estimates and spatially resolved column measurements, are integrated. A unique aspect of this work is the first-time description of plume height estimations derived from ground and column NH3 concentration measurements aimed at uncertainty reduction. Initial validation tests indicated measurement errors between −31 % and +14 % on average, which was slightly larger than the estimated expanded uncertainty ranging from ± 12 % to ± 17 %. Application of the methodology to assess emission rates from farms of various sizes showed uncertainties between ± 21 % and ± 37 %, generally influenced by systematic wind uncertainties and random errors. The method demonstrates the capacity to measure NH3 emissions from both small (∼ 0.5–1 kg h−1) and large (∼ 100 kg h−1) sources in high-density farming areas. Generally, the SOF method provided an expanded uncertainty below 30 % in measuring NH3 emissions from livestock production, which could be further improved by adhering to best application practices. This paper's findings offer the potential for broader applications, such as measuring NH3 fluxes from fertilized fields and in the oil and gas sector. However, these applications would require further research to adapt and refine the methodologies for these specific contexts.