Phenolic compounds are secondary metabolites widely distributed among plants, with bioactive properties, especially antioxidant activity. The search for sustainable extraction methods has driven the use of natural deep eutectic solvents (NaDESs), formed by combinations of natural compounds, such as organic acids, sugars, alcohols, and amino acids. This study optimized NaDES (sorbitol, citric acid, and glycine) efficiency and compared it to that of 70% methanol solution in extracting total soluble phenolic compounds (TSPCs) from six flours matrices—corn, buckwheat, biofortified orange sweet potato, red lentil, Sudan grass, and chickpea—before and after thermoplastic extrusion cooking. Quantification was performed using the Folin–Ciocalteu method, with statistical analysis at the 10% significance level. In general, the methanolic extracts showed higher TSPC levels in the raw materials, whereas the levels were higher in NaDESs for legumes. After extrusion, a reduction in the TSPC levels was observed, except in the sweet potato. Multivariate analysis (PLS-DA and heatmap) distinguished the raw and extruded samples, revealing structural and chemical changes from thermal processing. The AGREE scores were 0.7 (NaDES) and 0.54 (methanol), favoring NaDES. The BAGI score (75.0) confirmed the method’s robustness and suitability for sustainable analytical applications.

Seed germination induces profound physiological and metabolic changes that promote the synthesis and accumulation of bioactive metabolites in cereal grains. However, the combined effects of germination time and temperature on these responses in black rice (Oryza sativa L.) remain poorly understood. This study investigated how controlled germination modulates the accumulation of GABA (γ-aminobutyric acid) and phenolic metabolites and identified optimal conditions for obtaining bioactive-rich water-soluble extracts. A central composite design was applied by varying germination time (24–96 h) and temperature (14–32 °C). Germinated flours and their corresponding water-soluble extracts were analyzed for GABA, total soluble phenolics, flavonoids, anthocyanins, proanthocyanidins, and oxygen radical absorbance capacity (ORAC). Response surface methodology, desirability analysis, principal component analysis, heatmap, and partial least squares discriminant analysis were used to characterize metabolic responses and optimize germination conditions. Germination significantly altered metabolite accumulation, with higher GABA levels observed at lower temperatures, whereas phenolic metabolites showed distinct responses to the interaction between time and temperature. Multivariate analyses revealed clear metabolic differentiation among germination treatments. Multi-response optimization identified 27 h and 19.7 °C as the optimal germination conditions. These findings demonstrate that controlled germination modulates the bioactive profile of black rice, enhancing phytochemical accumulation and supporting the production of bioactive-rich water-soluble extracts.