Now online! A host-filtering and decontamination pipeline was benchmarked and applied to 16,369 tumor genomes, providing a high-resolution atlas of the cancer microbiome. Although most cancer types lacked a detectable microbiome, orodigestive cancers harbored complex multi-kingdom microbial communities that varied by site, subtype, and somatic mutation burden, linking the tumor microbiome to host phenotype and tumor genomic context.