Seed coat fragments that remain in lint after the ginning process decrease spinning efficiency at the textile mill, and ultimately reduce the quality of finished goods. An experiment was conducted to determine the impact harvest and seed cotton cleaning treatments had on the fiber quality attributes of an upland cultivar known to have fragile seed coats. Three harvester treatments examined spindle size (diameter) and speed (rpm) on the picker: 13-mm (1/2-in) spindles operated at 2000 rpm; and 14-mm (9/16-in) spindles operated at either 1500 or 2400 rpm. Three seed cotton cleaning treatments varied the number of seed cotton cleaners from none to twice as many as customarily used. Seed coat nep count in the fiber as determined by AFIS was used as an indicator of seed coat fragment levels. Results showed that using a larger spindle diameter lowered seed cotton trash content at the wagon and feeder, produced less short fiber, and a higher color grade: however, seed coat nep count was not different. Increasing the number of seed cotton cleaners reduced trash content in the seed cotton (at the feeder), cottonseed, and fiber and improved color grade but not seed coat nep count. All other fiber and cottonseed properties were not different among harvesting or seed cotton cleaning treatments. It appeared that neither spindle size, spindle speed, nor increased seed cotton cleaning helped manage seed coat fragments. Future research is planned to examine possible methods to reduce seed coat fragments through modifications at the lint cleaner.