The ginning process has an effect on fiber quality. Avoiding fiber quality deterioration due to mistune or overspeed is crucial, especially in west and central Africa where value chains are highly dependent on prices paid for premium fiber quality. Indeed, fiber classification alone does not permit a reliable measurement of ginning impact, as it depends on many factors such as incoming seed cotton quality, equipment type, number, and settings within each ginning process stage. This study describes a sampling and analysis method precise enough to detect any commercial impact on fiber quality at each main ginning stage. It is based on fiber quality characteristic measurements before and after each main stage: seed cotton cleaning, ginning, and lint cleaning. The sampling and testing protocol was applied in Mali in seven industrial gins during the 2015–2016 ginning season. Seed cotton samples were taken before and after the seed cotton cleaning stage, and fiber samples before and after the lint cleaning stage. Seed cotton samples were ginned with a reference saw micro-gin. The precision of fiber characterization was measured by replicating twice each fiber sample characterization in a laboratory meeting the international standards. Based on the variability measured in Mali, we determined for each fiber characteristic the number of replicates required to detect any commercially harmful impact. Growing and ginning conditions in Mali are representative of those in west and central Africa. Based on this method, one needs to develop an on-line tool to measure fiber quality at every stage of industrial ginning.