Farmer's dominance depends on seed processing practices that allow seed longevity and sanity throughout storage. In organic systems, seeds cannot be exposed to chemical pesticides. Therefore, organic seed treatment must be conducted by applying techniques which do not contaminate seeds and that can provide physiological and sanitary quality, and also a safe storage. This work aimed to evaluate the physiological and sanitary quality of pumpkin seeds frozen at -18°C and cooled at 15°C, for 36 h and 7 days in polyethylene terephthalate (PET) bottles and in plastic bags with vacuum. Results showed that freezing seeds at -18°C for 36 h in PET bottle provided an increase in the first count of germination and seedling length reduction. The physiological and sanitary qualities of pumpkin seeds frozen at -18°C for 36 h in PET bottle and stored for up to six months under ambient conditions and in a cold chamber were also evaluated. Refrigerated storage provided increased seed viability as compared to ambient storage. In the sixth month of storage, a reduction of the genera Aspergillus and Penicillium occurred in both environments.