Soft rot Pectobacteriaceae (SRP) are the causative agents of soft rot and blackleg in potato. In this study, we investigated if potato seed lots of the same cultivar, but originating from different fields, inoculated with the same density of SRP and planted in the same field, showed differences in blackleg disease incidence. We tested if these differences were correlated with the microbial community composition in tuber, and the soil where the mother tubers were grown, as the microbiome is known to play a large role in plant disease resistance. We found that tubers from seed lots with a high disease incidence had a different microbial community composition than tubers from seed lots with a low disease incidence. Several taxa could be identified that were on average more abundant in seed lots with a low disease incidence. However, the taxa that differed in abundance were different between the two growing seasons. Most of the taxa that differed in abundance between seed lots with high and low disease incidence were also present in the soil of the fields from which the tubers originated. However, the taxa did not differ in abundance between the different fields. This raises the question as to how these taxa are recruited by the tuber.