Avian coccidiosis remains one of the major parasitic diseases that threaten the global poultry industry. Since prevention is superior to treatment, this study focuses on eliminating the infection outside the host. To determine their effect on the viability of Eimeria tenella oocysts in vitro, allicin and alcoholic garlic extract, which are natural, less toxic, and inexpensive products, were compared to KOH 5% (chemical disinfectant) using an in vitro culture system. Three concentrations of allicin (45, 90, and 180 mg/mL) and alcoholic garlic extract (90, 180, and 360 mg/mL, were used. Subsequently, destructive and sporulation-inhibiting effects on Eimeria oocysts were detected using light and electron microscopy. Young chickens were infected with treated sporulated oocysts to determine their effect on infectivity. After 7 days pi, the percentage of excreted oocysts (oocyst shedding) was determined, and the chickens were slaughtered for histopathological examination of the cecal tissues. Under an electron microscope, allicin at a concentration of 180 mg/mL and alcoholic garlic extract at a concentration of 360 mg/mL demonstrate a high oocysticidal activity with severe destruction of the oocyst wall and the appearance of pores. In addition, both concentrations directly affected the infectivity of sporulated oocysts by reducing the shedding of oocysts and the pathological lesions of infected young chickens. We concluded that the ability of Allicin and alcoholic garlic extract to eliminate Eimeria oocysts makes them superior to chemical disinfectants as a disinfectant.