The poultry industry is one of the fastest-growing subsectors in agriculture, serving as a primary source of protein for the increasing global population. However, chickens carry many fatal diseases that compromise their welfare and negatively affect productivity. Among these, coccidiosis, an intestinal disease caused by Eimeria protozoan parasites, affects multiple animal species and represents a major threat to the poultry industry. Eimeria parasites invade the host cell through a distinctive process, depending on gliding motility, and require a transmembrane link between the host cell and parasite cytoskeleton. Each species invades intestinal epithelial cells in a specific gut region, leading to varying tissue damage and morbidity levels. Understanding the preliminary host-parasite interactions is crucial to revealing Eimeria species' conduct and cellular immune responses mediating the primary and secondary coccidian infection, which can inform the development of effective immunological strategies. The interaction between Eimeria invasion proteins and intestinal epithelial cells provokes a moderate immune response marked by elevated IFN-γ and IL-10 production in chickens. In this review, we highlight recent breakthroughs in understanding the Eimeria parasites that affect the host intestinal tract, emphasizing parasite invasion mechanisms, transmission dynamics, host immune responses, coccidian control mechanisms, and the interaction between host microbiota and coccidia. In conclusion, advancing our understanding of Eimeria invasion mechanisms and coccidia control requires a complex approach that combines cutting-edge molecular insights with innovative therapeutic strategies.