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The quality and productivity of maize crops are functions of the planting materials and crop management practices. However, the quality and storage practices of farm-saved maize seed, used by more than 70% of smallholder farmers in Tanzania, are less well studied. This study aimed to assess the status of maize seed systems, storage practices, and the quality of stored seeds in the Kilosa, Gairo, and Mvomero districts of the Morogoro region. A multi-stage stratified sampling approach was applied to survey 240 maize farmers across 11 villages in the three districts. Data were collected through semi-structured questionnaires and focus group discussions. Survey data were analysed using R software using a chi-square test ( p ≤ 0.05) to examine relationships between variables. In addition, a second study was conducted using a 3 × 3 factorial experiment arranged in a completely randomised design (CRD). Maize seed samples from the three most common storage materials were collected at harvest and after 3 months of storage for laboratory analysis of seed quality parameters: germination percentage, vigour index, and moisture content. The data were subjected to ANOVA followed by Tukey’s HSD test ( p ≤ 0.05) in R software. Results revealed that 56.2% of farmers used informal seed systems, and 70.8% engaged in seed recycling due to financial constraints. Education level significantly influenced the choice of maize seed system ( p = 0.004), maize cultivar ( p = 0.025), and maize seed recycling practice ( p = 0.023). Polypropylene bags (with and without insecticide) and hermetic bags were the most common storage materials. The hermetic bag maintained a higher seed germination rate (86.8%) than the polypropylene bag without insecticide (81.8%). Hermetic bags are therefore recommended over polypropylene bags (with and without insecticide) for enhancing maize seed storage. Capacity building on seed systems should prioritise farmer education as it significantly determines the seed systems and handling practices adopted.