Seeds harbor diverse microbial communities important for plant growth and health. During germination, seed exudation triggers intense microbial competition, shaping the communities transmitted to seedlings. This study explores the role of the bacterial type VI secretion system (T6SS)-mediated interference competition in seed microbiota transmission to seedlings. Distribution of T6SS within 180 genome sequences of seed-borne bacterial strains enabled the construction of SynCom with different levels of phylogenetic diversity and T6SS richness. These SynComs were inoculated withStenotrophomonas rhizophilaCFBP13503, a bacterial strain which possesses a T6SS activein vitroandin planta. SynComs compositions were comparedin vitrowith CFBP13503 wild-type strain or its isogenic T6SS-deficient mutant. Additionally, the effects of T6SS on the whole bacterial community dynamics during seed-to-seedling transmission were examined following seed-inoculation. The T6SS ofS. rhizophilaCFBP13503 targeted a large number of bacteria belonging to 5 different families The phylogenetic proximity and metabolic overlap of preys with CFBP13503 partly explains the sensitivity phenotype observed. The T6SS of CFBP13503 modulates the abundance of a few specific bacterial taxa during seed-to-seedling transmission depending on seed microbial initial inoculation and plant stage. Depending on the sensitivity of the co-inoculated competitors, the T6SS can provide a competitive advantage to CFBP13503, resulting in an increase in population size.