Microsporidiosis of adult honeybees caused by Nosema apis and Nosema ceranae is a common worldwide disease with negative impacts on colony strength and productivity. Few options are available to control the disease at present. The role of the queen in bee population renewal and the replacement of bee losses due to Nosema infection is vital to maintain colony homeostasis. Younger queens have a greater egg laying potential and they produce a greater proportion of uninfected newly eclosed bees to compensate for adult bee losses; hence, a field study was performed to determine the effect of induced queen replacement on Nosema infection in honey bee colonies, focusing on colony strength and honey production. In addition, the impact of long-term Nosema infection of a colony on the ovaries and ventriculus of the queen was evaluated. Queen replacement resulted in a remarkable decrease in the rates of Nosema infection, comparable with that induced by fumagillin treatment. However, detrimental effects on the overall colony state were observed due to the combined effects of stressors such as the queenless condition, lack of brood and high infection rates. The ovaries and ventriculi of queens in infected colonies revealed no signs of Nosema infection and there were no lesions in ovarioles or epithelial ventricular cells.