This study investigates the mechanisms governing the formation and transfer of microbial communities associated with the honey bee (Apis mellifera L.) superorganism, focusing on the interplay between plant, in-hive, and bee environments. By analyzing 16S rRNA sequencing data from multiple public datasets through bioinformatics and statistical modeling, we characterized the structure and transmission pathways of these microbiota. Our analysis reveals that each environment hosts a distinct and specialized microbial community, with significant barriers to free microbial exchange. Alpha and beta-diversity analyses confirmed the uniqueness of the bee gut microbiota and the mixed, intermediate nature of the honey microbiome. Structural equation modeling identified that direct microbial transfer from plants to bees is negligible. Instead, honey serves as an obligate intermediary and selective filter, with microorganisms transitioning from plants to honey before a lower-probability transfer to bees occurs. Furthermore, we identified key bacterial taxa, including Apilactobacillus kunkeei, Acinetobacter, and Pseudomonas, that potentially act as generalists capable of persisting across multiple environments. These findings underscore the possibility of the selective bacterial transfer between hives, which may play roles in both pathogens transfer and maintaining hive microbiome stability.