Nosema ceranae is an intestinal parasite frequently found in Apis mellifera colonies. This parasite belongs to Microsporidia, a group of obligate intracellular parasites known to be strongly dependent on their host for energy and resources. Previous studies have shown that N. ceranae could alter several metabolic pathways, including those involved in the nutrient storage. To explore the impact of N. ceranae on the fat body reserves, newly emerged summer bees were experimentally infected, and we measured (1) the lipid percentage of the abdominal fat body at 2-, 7- and 14-days post-inoculation (p.i.) using diethyl ether lipid extraction, (2) the triglyceride and protein concentrations by spectrophotometric assay methods, and (3) the amount of intracellular lipid droplets in trophocytes at 14- and 21-days p.i. using Nile Red staining. Comparing the three methods used to evaluate lipid stores, our data revealed that Nile Red staining seemed to be the simplest, fastest and reliable method. Our results first revealed that the percentage of fat body lipids significantly decreased in infected bees at D14 p.i. The protein stores did not seem to be affected by the infection, while triglyceride concentration was reduced by 30% and lipid droplet amount by 50% at D14 p.i. Finally, a similar decrease in lipid droplet reserves in response to N. ceranae infection was observed in bees collected in fall.