Vairimorpha (Microsporidia: Nosematidae)is a microsporidian that infects honey bees especially in winter. Fumagillin can reduce infections, but whether overwintering survival is improved is unclear. The diet also may influence the severity of Nosema infections. We examined the relationship between Nosema and colony size and survival in hives overwintered in cold storage facilities. In year 1, no Fumagillin treatments were applied. Colony size and survival after cold storage and almond bloom were comparable between groups with high and low pre-cold storage infections. In year 2, size and survival were compared among colonies with and without Fumagillin treatment that were fed either pollen or protein supplement prior to overwintering. Colonies treated with Fumagillin had lower spore numbers than untreated, but colony sizes and survival were similar among the treatments. However, more colonies with zero spores per bee could be rented for almond pollination and were alive after bloom than those averaging >1 million spores per bee. Fat body metrics can affect overwintering success. In both years, fat body weights and protein concentrations increased, and lipid concentrations decreased while bees were in cold storage. Fat body metrics did not differ with Nosema infection levels. However, Fumagillin negatively affected pre-cold storage fat body protein concentrations and colony sizes after cold storage and almond bloom. Treating with Fumagillin before overwintering in cold storage might result in greater colony survival if spore numbers are high, but undetectable or even negative effects when spore numbers are low.