Zoonotic, pathogenic protozoa are a serious public health concern. Three common species, Cryptosporidium parvum, Giardia enterica, and Toxoplasma gondii have been detected in commercial oysters. Current methods of detecting protozoa in shellfish are not standardized and few are able to simultaneously identify multiple species of interest. Here we present a bioinformatics pipeline to process 18S rRNA amplicons extracted from oyster matrices for the purpose of detecting protozoan pathogens. The pipeline was successfully applied for detection of G. enterica cysts and C. parvum and T. gondii oocysts spiked into whole oyster homogenates and hemolymph. These results indicate that 18S rRNA metabarcoding coupled with the validated pipeline could be tested for monitoring wild oysters contaminated with protozoan pathogens. While this study focused on detecting three parasites of interest, the multispecies identification abilities of this method make it an ideal screening tool for a broad range of protozoan pathogens in shellfish.