The industry of vegetable processing generates large amounts of by-products, which often emerge seasonally and are susceptible to microbial degradation. Inadequate management of this biomass results in the loss of valuable compounds that are found in vegetable by-products that can be recovered. Considering the possibility of using waste, scientists are trying to reuse discarded biomass and residues to create a product of higher value than those processed. The by-products from the vegetable industry can provide an added source of fibre, essential oils, proteins, lipids, carbohydrates, and bioactive compounds, such as phenolics. Many of these compounds have bioactive properties, such as antioxidative, antimicrobial, and anti-inflammatory activity, which could be used, especially in the prevention or treatment of lifestyle diseases connected with the intestinal milieu, including dysbiosis and immune-mediated diseases resulting in inflammation. This review summarises the key aspects of the health-promoting value of by-products and their bioactive compounds derived from fresh or processed biomass and extracts. In this paper, the relevance of side streams as a source of beneficial compounds with the potential for promoting health is considered, particularly their impact on the microbiota, immune system, and gut milieu because all of these fields interact closely to affect host nutrition, prevent chronic inflammation, and provide resistance to some pathogens.