Intracellular symbiosis is considered to be a driving force in eukaryotic cell evolution. In insects, little is known about the molecular bases of the bacteria‐bearing host cells (bacteriocytes), particularly in the initial steps of symbiosis, where the bacterial genome has not experienced severe gene deletions because of evolutionary constraints associated with intracellular and vertical transmission. Here, we have applied polymerase chain reaction (PCR)‐subtracted cDNA and reverse Northern analysis on the bacteriocytes of a recently established endosymbiosis, the weevil Sitophilus zeamais, to discover genes of potential relevance to bacteriocyte genetics. We provide a broad characterization of bacteriocyte transcriptional responses to intracellular bacteria, including pathways covering metabolism‐transport‐stress (MTS), cell signalling and trafficking, growth and apoptosis, as well as innate immunity. MTS genes show an intriguing diabetes‐like pathogenic profile associated with increased stress, as indicated by high levels of upregulations of carbohydrate transporters, aldose reductases and stress‐related genes. A high‐performance liquid chromatography (HPLC) analysis of tissue carbohydrate contents highlighted an increased carbohydrate assimilation in symbiotic insects and the prevalence of a polyol biosynthetic pathway, as indicated by the accumulation of sorbitol, mannitol and fructose in the bacteriocytes. These findings provide the first genetic perspectives on the nature of the interaction between insect and cooperative bacteria. They unravel the profound insect bacteriocyte stress associated with increased metabolism and cell trafficking, and they shed light on the potential role of the innate immunity during the pathogeny‐mutualism transition at the initial stage of insect symbiogenesis.