Through increased awareness and improved diagnostics, microsporidiosis has now been identified in a broader range of human populations; however current therapies are inconsistently effective. Recently, probiotics were determined as means for the control of intestinal parasitic infections through their secretory products; bacteriocins. This is the first study on the effect of bacteriocin produced by Lactobacillus acidophilus CH1 bacteriocin, with or without gold nanoparticles (Au-NPs), against intestinal microsporidiosis in immunosuppressed mice. Fecal and intestinal spore loads, besides viability, extrusion and infectivity of spores from treated animals were assessed. Results showed that the anti-microsporidial effects of bacteriocin were significantly potent. This efficiency was further potentiated upon conjugating bacteriocins with Au-NPs, as it induced a strikingly sustained reduction in fecal spore shedding after cessation of therapy by 1 week (94.26%). Furthermore, reduction in intestinal spore load was highest in bacteriocin/Au-NPs-inoculated mice (89.7%) followed by bacteriocin-inoculated group (73.5%). Spores encountered from stool of bacteriocin/Au-NPs group showed 92.4% viability, versus 93.7% in bacteriocin group. Spore extrusion and infectivity were most inhibited by exposure to bacteriocin/Au-NPs. Safety of bacteriocin/Au-NPs was also verified. Thus, considering the results of the present work, L. acidophilus CH1-derived bacteriocin can present a powerful safe therapy against intestinal microsporidiosis.