Endocrine disrupting chemicals (EDCs) that act as xenoestrogens are natural and synthetic chemicals widely present in food products, industrial products, and the environment. Such compounds can activate or inhibit normal hormonal pathways by binding to steroid and non-steroid receptors. It is becomingly apparent that resident bacteria in the gut and elsewhere in the body can dramatically influence host responses. As such, increasing number of studies have examined how EDCs affect the gut microbiome in a range of animal species. This review article will examine what is known about how various xenoestrogens, including bisphenol A (BPA), phthalates, and phytoestrogens, affect the gut microbiome in vertebrate species, any known secondary host effects, such as through alteration of gut metabolites, and future directions in the field.