Intestinal helminths, along with mutualistic microbes, have cohabited the intestine of mammals throughout evolution. Interactions between helminths, bacteria, and their mammalian hosts may shape not only host–helminth and host–microbiome interactions, but also the relationship between helminths and the microbiome. This ‘ménage à trois’ situation may not be completely balanced in that it may favor either the host or the parasite, possibly at the cost of the other partner. Similarly, helminths may favor the establishment of a particular microbiome with either positive or negative consequences for the overall health and well-being of the host. Recent studies indicate that infection with intestinal helminths can and does impact the intestinal microbiome, with important consequences for each partner in this tripartite relationship. In humans, both cross-sectional and case-control studies performed in regions endemic for intestinal helminths provided evidence that infection may alter fecal bacterial communities. In mice, infection with the large intestinal helminth Trichuris muris can promote colonization resistance against the pathogenic bacterium Bacteroides vulgatus by promoting the growth of nonpathogenic bacterial species. In mice, infection with the small intestinal helminth Heligmosomoides polygyrus has been shown to alter the cecal microbiome and results in greater availability of bacterially derived metabolites, SCFAs, that function to dampen allergic responses.