Neonicotinoids are among the most widely used systemic pesticides across the world. These chemicals have gathered significant attention for their potential adverse impacts on non-target organisms. Clothianidin is a novel neonicotinoid pesticide, employed globally to control sucking and chewing types of pests. In nature, various non-target organisms can be exposed to this chemical through contaminated food, water, and air. Nonetheless, extensive investigations demonstrating the sub-lethal impacts of clothianidin on non-target entities are limited. Hence, the present study was aimed to unravel the chronic sub-lethal impacts (LC50 0.74 μg/mL) of clothianidin on a non-target organism, Drosophila melanogaster. The study parameters involved multiple tiers of life ranging from organismal level to the sub-cellular level. 1st instar larvae were exposed to the six sub-lethal concentrations viz. 0.05, 0.06, 0.07, 0.08, 0.09, and 0.1 μg/mL of clothianidin till their 3rd larval instar. Investigations involving organismal level have revealed clothianidin-induced significant reduction in the developmental duration, life span, phototaxis, and physical activities of the treated individuals. Interestingly, the tested compound has also altered the compound eye morphology of treated flies. Study was extended to the tissue and cellular levels where reduced cell viability in gut, brain, and fat body was apparent. Additionally, increased ROS production, nuclear disorganization, and higher lipid deposition were evident in gut of exposed individuals. Study was further extended to the sub-cellular level where chronic exposure to clothianidin up-regulated the major oxidative stress markers such as lipid peroxidation, protein carbonylation, HSP-70, SOD, catalase, GSH, and thioredoxin reductase. Furthermore, the activities of detoxifying enzymes such as CYP4501A1 and GST were also altered. Chronic exposure to clothianidin also triggered DNA fragmentation in treated larvae. In essence, results of this multi-level study depict the ROS-mediated toxicity of clothianidin on a non-target organism, D. melanogaster.