Nosema ceranae is a damaging parasite of the honey bee, Apis mellifera. The only registered treatment is the antibiotic fumagillin. Thirteen nutraceuticals, three prebiotics and three probiotics were examined as novel alternative compounds for controlling N. ceranae. Caged bees were inoculated with N. ceranae spores, and treatments were administered in sugar syrup. The most effective nutraceuticals were sulforaphane (from cruciferous vegetables), completely eliminating N. ceranae spores but causing 100% bee mortality at higher doses, and naringenin (from citrus), reducing spores by 70% but only causing 10% bee mortality. The most effective prebiotic was acacia gum, reducing spores by 50% but causing over 60% bee mortality. The most effective probiotic was Protexin Concentrate© single-strain (ProtexinC1), reducing spores by 50% and significantly increasing bee survival above uninfected, Nosema-free control bees. Future research on reducing sulforaphane and acacia gum toxicity is needed. Naringenin and ProtexinC1, however, are promising new controls for N. ceranae.