Quality seed is a prerequisite to uniform stand establishment, which contributes to higher crop yield. However, prevalence of poor-quality cottonseed with high moisture content due to suboptimal harvesting and postharvest practices is the primary reason for crop-stand failure in developing countries. The present study evaluated the effects of harvesting environment, drying method and storage conditions on seed quality of transgenic (FH-142) and non-transgenic (FH-942) genotypes of cotton (Gossypium hirsutum L.) cultivated in Pakistan. Both genotypes were picked three times at monthly intervals during the cropping season and subjected to a ginning process. Seed was then dried in the sun or with desiccant zeolite beads, and stored for 5 months in cloth or hermetic bags at room temperature or in paper bags at 10°C. The efficiency of storage systems was evaluated by estimating moisture content and germination potential periodically in the storehouse and later under field conditions. Both genotypes exhibited better seed quality attributes at the first picking, and zeolite beads dried seed to lowest moisture content more quickly than sun-drying. Seeds of both genotypes stored hermetically retained the lowest moisture content, maximum germination potential, and lower fatty acid contents throughout the storage period, as well as performing significantly better in the field by exhibiting early and uniform stand establishment, more fruiting branches and bolls, and higher yield. Thus, use of zeolite beads in post-harvest drying followed by hermetic storage preserves cottonseed quality for longer, and leads to improved crop growth and yield of cotton. These practices will be useful for cotton farmers in developing countries.