A field experiment was conducted in Aleshtar, Iran during 2015-16 growing season to evaluate the effect of limited water supply during seed filling period on seed quality changes of Persian clover. The experiment was carried out as a 2×6 factorial with three replications. Irrigation systems including conventional (all root system was irrigated) and partial root-zone irrigation (half of root system exposed to dry soil and the other half was watered) and harvest time (initiated from 10 days after flowering (DAA) and continued on six occasions at 5-day intervals) were used as treatments. Germination percentage, seedling dry mass, electrical conductivity and 1000-seed mass were used as seed quality traits. Seed quality attributes were significantly affected by harvest time and irrigation system, but the interaction of irrigation system × harvest time was not significant. While seed mass and electrical conductivity were not significantly affected by irrigation system, seedling dry mass and germination percentage were reduced under deficit irrigation. Partial root-zone irrigation reduced seed quality, Persian clover needs to experience no water deficit during seed formation and maturation period to produce high quality and quantity seeds.