The gut microbiota sit at an important interface between the host and the environment, and are exposed to a multitude of nutritive and non-nutritive substances. These microbiota are critical to maintaining host health, but their supportive roles may be compromised in response to endogenous compounds. Numerous non-nutritive substances are introduced through contaminated foods, with three common groups of contaminants being bisphenols, phthalates, and mycotoxins. The former contaminants are commonly introduced through food and/or beverages packaged in plastic, while mycotoxins contaminate various crops used to feed livestock and humans alike. Each group of contaminants have been shown to shift microbial communities following exposure; however, specific patterns in microbial responses have yet to be identified, and little is known about the capacity of the microbiota to metabolize these contaminants. This review characterizes the state of existing research related to gut microbial responses to and biotransformation of bisphenols, phthalates, and mycotoxins. Collectively, we highlight the need to identify consistent, contaminant-specific responses in microbial shifts, whether these community alterations are a result of contaminant effects on the host or microbiota directly, and to identify the extent of contaminant biotransformation by microbiota, including if these transformations occur in physiologically relevant contexts.