Imidacloprid (IMD) may affect proteolysis, aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP), and global DNA methylation in honeybees. Queens, drones, and workers aged 1 or 20 days were exposed (free-flying colonies) to IMD (5 ppb and 200 ppb) in their diet. As a result, the colony depopulation did not occurred. IMD disturbed hemolymph/cuticle proteolysis; deactivated most of the cuticle protease inhibitors, activated hemolymph thiol and metal proteases and cuticle thiol proteases; downregulated ALP, ALT, AST; and increased DNA methylation in a caste- and age-dependent manner. The response in queens and workers differed, possibly due to eusocial evolution. Higher IMD dose had greater effects. The responses of ALP, ALT, AST, and DNA may reflect acceleration of biochemical senescence and epigenetic adaptation to IMD. All these biochemical side effects may lead to colony depopulation during future biotic/abiotic stress.