The gut microbiota plays a key role in health and disease, but it could be affected by various factors (diet, lifestyle, environment, genetics, etc.). Focusing on diet, while the role of the different styles and choices (Mediterranean vs. Western diet, vegan or vegetarian diets) has been extensively studied, there are a few comprehensive papers on the effects of additives and food processing. Therefore, the main goal of this manuscript is to propose an overview of the link between ultra-processed foods and the gut microbiota based on papers and data available in the literature. The literature search was performed on PubMed and Clinicaltrials.gov, and after the selection of the most relevant articles, the paper proposes a synopsis of the effects of some classes of additives (sweeteners, preservatives, emulsifiers, glutamate, etc.), as well as of some treatments, on the gut microbiota and some pathological conditions.