Interactions between multiple stressors have been implicated in elevated honeybee colony losses. Here, we extend our landscape-scale study on the effects of placement at clothianidin seed-treated oilseed rape fields on honeybees with an additional year and new data on honeybee colony development, swarming, mortality, pathogens and immune gene expression. Clothianidin residues in pollen, nectar and honeybees were consistently higher at clothianidin-treated fields, with large differences between fields and years. We found large variations in colony development and microbial composition and no observable negative impact of placement at clothianidin-treated fields. Clothianidin treatment was associated with an increase in brood, adult bees and Gilliamella apicola (beneficial gut symbiont) and a decrease in Aphid lethal paralysis virus and Black queen cell virus - particularly in the second year. The results suggest that at colony level, honeybees are relatively robust to the effects of clothianidin in real-world agricultural landscapes, with moderate, natural disease pressure.