Nosemosis is one of the most devastating diseases of Apis mellifera (Honey bees) caused by the single-celled spore-forming fungi Nosema apis, N. ceranae and N. neumanii, causing a severe loss on the colony vitality and productivity. Fumagillin, a MetAP2 inhibitor, was a certified treatment for controlling nosemosis, nevertheless, due to its deleterious effects on honey bees and humans, it is prohibited. So, searching for novel biological agents with affordable selectivity to target Nosema species infecting Apis mellifera, with nil toxicity to bees and humans is the main objective of this study. Nosema species were isolated from naturally infected honey bees. The methanolic extracts of Acacia nilotica, Elaeis guineensis, and Catharanthus roseus were tested to selectively control the growth of Nosema spp of honeybees. The spores of Nosema species were molecularly and morphologically identified. Among the tested plant extracts, the methanolic extracts (0.1%) of A. nilotica had the most activity towards Nosema spp causing about 37.8 and 32.5% reduction in the spores’ load at 5- and 9-days post-infection, respectively, compared to the untreated control. At 0.1%, the A. nilotica methanolic extract exhibited the highest inhibitory effect for Nosema spores, without any obvious bee mortality. Catharanthus roseus displayed a reduction of spores by 27.02%, with bee mortality rate of 27.02%. At 1% for 5 dpi, the A. nilotica extracts led to 18.18% bee mortality, while the C. roseus extracts resulted in 100% mortality, as revealed from the toxicity and quantification bioassays. So, the extracts of A. nilotica and C. roseus had a significant effect in controlling the N. apis and N. ceranae titer compared to the infected untreated control at both time points. The titer of N. apis and N. ceranae was noticeably decreased by more than 80% and 90%, in response to A. nilotica, compared to the control. From the metabolic profiling by GC–MS analysis, the most frequent active compounds of A. nilotica were 2,4,6-trihy-droxybenzoic acid, 1,2-dihydroxybenzene, myristic acid, and linoleic acid. These compounds were analyzed in silico to assess their binding affinity to the ATP binding protein, methionine aminopeptidase and polar tube protein of Nosema species as target enzymes. The compound 2,4,6-trihydroxybenzoic acid had the lowest energy to bind with ATP binding protein, methionine aminopeptidase and polar tube protein of Nosema, followed by 1,2-dihydroxybenzene and myristic acid, compared to fumagilin. So, from the experimental and molecular docking analysis, the extracts of A. nilotica had the highest activity to attack the cellular growth machinery of Nosema species without an obvious effect to the honeybees, ensuring their prospective promising application.