The quality of cotton fiber observed at classing depends on the production conditions (soil, variety, climate, and crop management practices, including harvesting technique) and on the ginning conditions (seed-cotton cleaning, ginning, and lint cleaning). Thus, when lint quality is monitored, variations in seed-cotton quality may be confused with the impact of variations in ginning conditions. So, rather than measuring the quality of the cotton leaving the ginning mill, we propose measuring the impact of ginning conditions on the difference in quality between a batch of cotton ginned in the mill and a sample of the same batch ginned using micro-ginning equipment. By comparing 11 industrial ginning mills with the micro-ginning equipment used as a control, this feasibility study evaluated the impact of ginning conditions in an experiment on 119 seed-cotton modules in Mali throughout the 2014–2015 season. Based on this comparison, data analysis showed that the ginning process did have an impact on cotton quality, that the impact varied with the date, and that it was only linked to ginning conditions. Conversely, no alert concerning the impact of industrial ginning conditions was issued based on the results of the evaluation of the quality of fiber samples from industrial ginning mills alone.