In light of the continuous increase in organic agriculture, the availability of organic seeds has gained a lot of importance. Especially since the new EU organic regulation came into force on 1 January 2022, proposing reducing the possibility of using untreated conventional seeds in the absence of organic seeds in the future. At the same time, the breeding of tolerant, resistant and adapted varieties is at the basis of organic production as is research to improve seed production and seed quality. In this study, we investigated seed production of 8 tomato genotypes. The aim was to see whether different fruit harvesting frequencies affect seed quality and germination rate. The hypotheses we tested were (i) whether regularly removing fruits from the field would affect total fruit and seed harvest, (ii) whether storage of fruits and (iii) their ripening stage at harvest, had an impact on seed germination. Our results show that while seed production differs between genotypes and extraction time-points, different harvesting procedures, and with that different fruit maturity levels, did not affect thousand-seed weight and seed germination; these findings benefit both small and larger-scale seed producers.