In alignment with Hippocrates’ aphorisms “Let food be your medicine and medicine be your food” and “All diseases begin in the gut”, recent studies have suggested that healthy diets should include fermented foods to temporally enhance live microorganisms in our gut. As a result, consumers are now demanding this type of food and fermented food has gained popularity. However, certain sectors of population, such as those allergic to milk proteins, lactose intolerant and strict vegetarians, cannot consume dairy products. Therefore, a need has arisen in order to offer consumers an alternative to fermented dairy products by exploring new non-dairy matrices as probiotics carriers. Accordingly, this review aims to explore the benefits of different fermented non-dairy beverages (legume, cereal, pseudocereal, fruit and vegetable), as potential carriers of bioactive compounds (generated during the fermentation process), prebiotics and different probiotic bacteria, providing protection to ensure that their viability is in the range of 106–107 CFU/mL at the consumption time, in order that they reach the intestine in high amounts and improve human health through modulation of the gut microbiome.