Willow (Salix spp.) trees, found worldwide, contain secondary metabolites that are valuable as dietary supplements for animal feed and as anti-parasitic compounds. We quantified secondary metabolites (phenolic, flavonoids, and salicylic acid) in ethanolic extracts from leaves and branches of three Salix acmophylla genotypes and investigated their potential to inhibit Eimeria sp. sporulation, a major concern in ruminants. The total phenolic content of willow leaves and branches was similar in two of three different genotypes. The total flavonoid content of the branches was significantly higher than that of leaves of the same genotype; however, the salicylic acid content was significantly higher in leaves than in branches. Importantly, all extracts exhibited significant inhibition of Eimeria sporulation, where over 70% inhibition was obtained at concentrations as low as 750 ppm. The sporulation inhibition by branch or leaf extracts exceeded 80% for leaves and 90% for branches at concentrations above 1250 ppm. The study highlights the potential of using Salix extracts as bioactive compounds for biological control of coccidiosis in ruminants and emphasizes the importance of genotype-specific variations in secondary metabolite profiles. We conclude that all parts of S. acmophylla can provide secondary metabolites that act as a coccidiostat to treat Eimeria in goats.