Currently, the European Commission through the Green Pact (the Green Deal) has indicated that food production must be sustainable considering climate change, avoiding the loss of biodiversity, and minimizing residues and food loss/waste. To address these challenges, the 2030 Agenda promotes research on healthy, accessible, and sustainable food, in which consideration of food effects on the human microbiome plays a crucial role due to its close relationship with human health. Food loss is one of the biggest problems faced by the current food system with negative economic and nutritional impacts and a large environmental footprint. Since fruit, vegetable, and nut by-products are good natural sources of macronutrients (carbohydrates, polysaccharides, proteins, fats, and fiber) and micronutrients (vitamins, minerals, and antioxidants), different valorization strategies have been applied. Among the various processes for stabilizing food losses, dehydration treatment combined with milling is a sustainable alternative for producing functional powdered ingredients with prebiotic effects on the gut microbiota. In this way, a wide range of prebiotics from different origins are being developed to improve human health through the modulation of the microbiome.