Investigations into seed microbiomes have unveiled intricate networks of microbial interactions that promote nutrient mobilization and uptake, significantly contributing to seedling vigor and resilience in diverse environmental conditions. Emerging evidence suggests that seed-borne microbes not only protect against pathogens but also influence plant developmental pathways, providing novel strategies for enhancing crop productivity via microbial inoculation. Moreover, these microbes might interfere with the endobiome of other plants, potentially suppressing competitor species, enhancing seedling growth, and increasing mortality. However, this effect is likely to be species-dependent, influenced by host plant species, microbial community composition, and environmental conditions. This implies that, in natural ecosystems, endobiome interference can be an important factor in plant-plant interactions. If validated through rigorous laboratory experiments and subsequent field trials, leveraging endobiome interference could offer a viable strategy to manage invasive or weedy plant species. This approach would be supported by integrated omics techniques, particularly genomics and metabolomics, to elucidate the genetic and metabolic contributions of seed microbiomes. Such insights could pave the way for precision microbiome engineering, ultimately optimizing agricultural yields while minimizing environmental impacts. This review article underscores the diverse and beneficial roles of seed microbiomes in plant biology, illustrating how ongoing research continues to deepen our understanding of their profound impacts on both plant health and the sustainability of agriculture.