Abstract Background Beyond carrying the plant embryo, seeds harbour intricate microbial communities whose transmission across successive plant generations can significantly influence the ecological and evolutionary dynamics of plant–microbe symbioses. The process of plant domestication has potential repercussions in genes involved in plant-microbiome interactions. However, the extent to which breeding can impact the seed microbiome is sparsely explored. Cannabis is a high-value crop but sparsely subjected to agricultural innovations established in other crop species during the last century. Here, we conduct a large-scale analysis of the bacterial seed microbiome of Cannabis across different domestication grades and investigate the potential of seed-associated endophytes as plant growth-promoting agents under both controlled and field conditions. Results Analysis of Cannabis seed endophyte composition and diversity across 46 plant genotypes revealed 813 different bacterial genera with a predominance of Gammaproteobacteria, Bacilli, Actinobacteria and Alphaproteobacteria but a genotype-specific microbiome. The assessment of domestication and breeding on microbial assembly revealed a higher bacterial diversity in low domestication genotypes (Shannon index, H′: 1.21 vs. 1.05) and a higher homogeneity in bacterial composition caused by line development. Further, a seed bacterial isolate (Bacillus frigoritolerans C1141) associated with low domestication genotypes, and with genes associated with bio-fertilization, bioremediation and phytohormone production, increased plant growth by 42.3% at the time of harvest, under field conditions. Conclusion This study addresses critical knowledge gaps related to the assembly of the Cannabis seed-endophytic microbiome. It reveals that Cannabis breeding is linked to alterations of seed microbial communities, which potentially led to the loss of bacteria with functional significance. These results highlight the importance of preserving seed microbiomes in plant breeding to support sustainable plant health and growth enhancement in Cannabis.