["Archives of Insect Biochemistry and Physiology, Volume 122, Issue 4, August 2026. ", "Honey bee brain transcriptomes distinctly separate larval and pupal stages, with increased transcriptional variability in pupae. Stage‐biased genes involve cuticular proteins, detoxification, regulatory factors, and microbiome‐linked metabolic and sensory pathways.\n\n\n\n\nABSTRACT\nThe larva‐to‐pupa transition in honey bees (Apis mellifera) involves extensive neural remodeling, yet the molecular dynamics of brain development and their relationship with the surrounding microbial environment remain poorly characterized. This study integrated brain transcriptomic profiling with comb‐associated metagenomic analysis to characterize stage‐specific molecular signatures during metamorphosis. RNA sequencing of larval and pupal brains was combined with honeycomb shotgun metagenomics from the same sample. Brain transcriptomes exhibited marked stage‐specific divergence. Pupae displayed downregulation of transcriptional regulators, ecdysone and insulin signaling, and growth‐related pathways, alongside upregulation of cuticular proteins, glutathione metabolism, and odorant‐binding proteins. Notably, numerous poorly annotated, lineage‐specific loci showed extreme stage‐specific regulation. In contrast, comb‐associated microbial communities remained globally stable across developmental stages, though supervised ordination identified stage‐discriminatory taxa, including core symbionts and opportunistic pathogens. Integrative network analysis revealed significant correlations between comb potential bee pathogens' abundances and brain transcripts involved in translation, stress response, and metabolic regulation. Our data suggest that honey bee neural maturation is primarily driven by intrinsic transcriptional reprogramming, while structured variation in the external microbial milieu correlates with host neural gene expression. Honeycomb microbiome shift should be the consequence of the environmental conditions changes and host developmental shifts. Their roles in that process, as well as the brood immune system‐comb microbiome interactions, may be part of future research."]