Seed quality is accessed by appropriate seed germination, seed moisture contents, insect/pathogen infestations and seed vigor. Seed storage conditions are essential to protect from deterioration. In this study, knowledge and practices of wheat and cotton seeds storage were accessed among commercial seed growers (CSGs) and non-commercial seeds growers (NCSGs) in the Vehari District of Pakistan, while samples of stored wheat and cotton seeds were also collected to assess the quality of stored seeds. Stored seeds in the study area were contaminated by a variety of fungi, with infestation percentages reaching 13% for wheat and 20.7% for cotton in seeds from NCSGs, compared to 9% (wheat) and 9.5% (cotton) in seeds from CSGs. The majority of seed growers (75.0%) did not have any training on seed storage. The growers (60.9%) were unaware that seed should not be stored in closed polythene bags and most (62.2%) were not well aware about seed-borne crop diseases. Most growers did not maintain the temperature and humidity of storage rooms (82.7%) and did not calculate the seed rate before sowing after seed germination tests (87.2%). However, seed dressing with fungicides was implemented by most farmers (69.9%). Controlling the temperature of the seed storage was significantly influenced by growers’ age, while controlling the humidity of the seed storage was significantly influenced by growers’ farming experience. Seed dressing with fungicides was positively associated with the graduation level of growers, while checking seed maturity was positively associated with the higher education (Master’s level) of growers. There was a lack of active information centers in the study areas and a lack of agricultural information provision to farmers. Awareness regarding bad-quality seeds should be initiated to increase growers’ knowledge. Training programs for providing adequate knowledge to growers and skills in seed storage should be organized. Legislation regarding the seed business and seed storage protective measures should be enforced to minimize problems by a seed-borne inoculum and deterioration of seed quality.