The valorization of the green aspects in the NMR-based foodomics leads to a green NMR-based foodomics approach [13], and it answers much more to the consumers’ “2.0” needs in terms of both food safety and quality, and sustainability. The green attribution has a twofold meaning: (1) green because, as it has been previously underlined, it involves “environment-friendly” chemicals (green chemistry). Castro-Puyana, et al. [85] demonstrate how foodomics can emerge as a green discipline by applying the basic concepts of Green Chemistry; (2) it is green because its challenge is to preserve sustainability, understood as a way of using and preserving what nature gives us in the most productive, environmentally safe way [85]. In the last years, foodomics started dealing with food ingredients able to improve our health, which means nutrients and BC. Thus, the extraction of BC from natural sources (such as plants, algae, food bio-waste, and food by-products, among others) and the quality analysis of functional foods (FF) is a key step in the foodomics workflow [16,85]. Food bio-waste or by-products from various sources can be fundamental for BC production and FF formulation. The high added value of these wastes is due to the content of BC, which, most of the time, is greater than in the edible part of the fruit [86]. For this reason, their proper waste management plays a vital role in the growth of food industries as they can contain valuable components such as polysaccharides, proteins, fats, fibers, and flavor compounds [87]. Azizan, et al. [88], by using 1H NMR, described bioactive metabolites from pineapple waste. These compounds have antioxidant capacity and they can inhibit the activity of a carbohydrate-active enzyme (α-glucosidase). In conclusion, it emerges that 3-methylglutaric acid, threonine, valine, and α-linolenic acid were the main contributors to the antioxidant activities, whereas epicatechin was responsible for the α-glucosidase inhibitory activity. The metabolic composition of cherimoya leaves (Annona cherimola Mill.) is also characterized by the presence of BC, such as phenolic compounds. It is a deciduous tree from the Annonaceae family, typical of Peru and Ecuador, and its fruits are largely produced in Spain [86]. In this case, the metabolic composition has been profiled by using the 1H NMR coupled with high-performance liquid chromatography coupled with time-of-flight mass spectrometry (HPLC-TOF-MS). The first (1H NMR) achieved 23 primary compounds, classified as amino acids, organic acids, carbohydrates, choline, phenolic acid derivatives, and flavonoids. The second (HPLC-TOF-MS) profiled 66 secondary metabolites among carbohydrates, amino acids, phenolic acids and derivatives, flavonoids, phenylpropanoids, and other polar compounds [86]. Similar antioxidant proprieties have also been identified in pistachio’s hard shells [89], blackcurrant skin [90], olive oil by-products [36,37], and date palm by-products [91]. In this last case, a strong antioxidant activity has also been attributed to date fruits, whose bioactive metabolites have been profiled by 1H NMR by Kadum, et al. [92]. In this work, five different cultivars have been compared to find the one with the most antioxidant activity. The obtained results demonstrated that the extract from the Piyarom variety had both the highest total phenolic and flavonoid content and exhibited good antioxidant activity. The metabolites responsible for the antioxidant activity, glucose, ascorbic acid, epicatechin, gallic acid, and citric acid, were successfully identified using 1H NMR-based metabolomics [92]. Among the BC, a particular interest is covered by prebiotics which are defined as “a nondigestible food ingredient that beneficially affects the host by selectively stimulating the growth and/or activity of one or a limited number of bacteria in the colon, and thus improves host health” [93,94]. To guarantee their bioactivity, prebiotics have to (i) be resistant to gastric acidity; (ii) avoid absorption in the gastrointestinal tract; (iii) not be subjected to enzymatic activity; (iv) be fermented by intestinal microflora to produce short-chain fatty acids, and (v) be a selective substrate for the growth of intestinal bacteria associated to human health and well-being [95,96]. The main prebiotic agents consist of nondigestible carbohydrates, such as polysaccharides (POS), oligosaccharides (OS), and soluble dietary fibers (mainly inulin) [96]. Prebiotic foods are largely requested on the market; thus, food industries are working on the development of sustainable bioprocesses that can guarantee OS from a waste of different sources [97,98,99]. An important resource of OS comes from lignocellulosic agricultural waste disposals. Apart from bioethanol generation, several studies demonstrated the conversion of lignocellulosic biomass into oligosaccharides, through both microbial fermentation and enzymatic hydrolysis, by microorganisms or enzymes [100,101]. Jana and Kango [100], through enzymatic hydrolysis, produced Mannooligosaccharides (MOS) from agricultural waste and their structural aspects were assessed using both 1H and 13C NMR spectroscopy. MOS respect all the important criteria of being a prebiotic as they are (i) gastrointestinal resistant, (ii) an active substrate promoting the growth of healthy bacteria, and (iii) able to confer antineoplastic properties without any cytotoxicity to normal cells [100]. The capability of prebiotics to enhance the growth of healthy bacteria can be exploited for the production of important physiological metabolites. An example is given by recent research from Hussin, et al. [102]. The study investigated the effect of different commercial prebiotics on enhancing natural gamma-aminobutyric acid (GABA) production in cultured yogurt. In addition, the metabolomics profile of the fermentation-derived biomolecules in yogurt has been obtained via NMR-based metabolomics. This approach was useful for comparing the major metabolite profile of freeze-dried GABA-rich yogurt (GY) and standard freeze-dried yogurt (SY). A total of 16 and 13 compounds were detected in GY and SY, respectively, and this difference may be due to the strain-specific metabolic activities of GABA [102]. According to pillar 1, described in the introduction, the choice of extraction methods to obtain any kind of BC is fundamental. Ethanol is an example of a green and sustainable bio-solvent as it is completely biodegradable and obtained by the fermentation of sugar-rich materials [103,104,105]. Also, dimethyl ether (DME), having a high cetane number and favorable carbon/oxygen ratio, emerged in the spotlight as a cleaner, environmentally friendly, and high-efficiency ignition fuel [106]. Thus, green solvents are among the preferred ones for extraction processes. For example, Cerulli, et al. [107], compared several ethanol-based solutions to find out the best one for the extraction of primary metabolites and inulin from “Carciofo di Paestum” (C. cardunculus subsp. scolymus) PGI heads. For the first time, a comprehensive investigation of green extracts was performed by LC-MS and NMR analysis to highlight the occurrence of both specialized and primary metabolites, respectively. Among all the extracts, hydroalcoholic, infusion, and decoction extracts were the most interesting, showing higher peaks for flavonoids, quinic acid derivatives, and inulin than MeOH extract [107]. Inulin is a polymer found widely distributed in nature as a plant storage carbohydrate with a high value in human nutrition. It has prebiotic proprieties for its resistance to digestion in the small intestine, it can be fermented by colonic microflora, and it can stimulate the proliferation of commensal bacteria [107]. Hence, artichokes are a source of prebiotic dietary fibers but also a source of metabolites with antioxidant activity associated with their high phenolic content [108].