There is growing concern that some managed and wild insect pollinator populations are in decline, potentially threatening biodiversity and sustainable food production on a global scale. In recent years, there has been increasing evidence that sub-lethal exposure to neurotoxic, neonicotinoid pesticides can negatively affect pollinator immunocompetence and amplify the effects of diseases, likely contributing to pollinator declines. Here we show that a range of non-neural tissues and haemocytes of the honeybee Apis mellifera express the nicotinic acetylcholine receptor that is the target of neonicotinoids. In addition, we demonstrate that the haemocytes, which form the cellular arm of the innate immune system, actively synthesize acetylcholine. This suggests the presence of a neural-independent acetylcholine-based immune signalling system in insects similar to that found in vertebrates. Lastly we establish that field-relevant doses of the neonicotinoid insecticide clothianidin alter this communication system. These findings provide a novel, mechanistically informed framework to understand the numerous siede-effects on insects of sub-lethal pesticide exposure, including immunosuppression. They support the growing evidence for acetylcholine-based immune regulation in invertebrates that operates independently of the nervous system.