A functional ingredient derived from extruded, germinated chia seeds would be an excellent substitute to improve the nutritional and nutraceutical quality of widely consumed foods in Mexico. The aim of this study was to create a functional ingredient with outstanding nutritional and nutraceutical value and microbiological safety by processing chia seeds using a combined germination and extrusion process under optimal conditions. The implementation of optimized germination and extrusion techniques was hypothesized to boost the nutritional value, phenolic compounds, γ-aminobutyric acid (GABA), antioxidant activity, in vitro antihypertensive potential, and microbiological stability of the functional flour obtained from chia seeds. Germinated chia flour (GCF) was produced under optimized germination conditions (21 °C for 157 h). To determine the optimal conditions for GCF extrusion, the response surface methodology was used. A central composite rotatable design was applied with two factors [extrusion temperature (ET, 50–160 °C) and screw velocity (SV, 50–240 rpm)] and five levels. Total phenolic compounds (TPC), antioxidant activity (AoxA), and in vitro protein digestibility (IVPD) were selected as response variables. The best combination of extrusion process variables to produce extruded germinated chia flour (EGCF) with maximum TPC, AoxA, and IVPD values was ET = 147 °C and SV = 170 rpm. EGCF had higher protein content (88 %), total dietary fiber (13 %), phenolic compounds (57 %), GABA (933 %), and antioxidant activity (2,2’-azino-bis(3-ethylbenzothiazoline-6-sulfonic) acid (ABTS), 110 %; 2,2-diphenyl-1-picrylhydrazyl (DPPH), 114 %) than raw chia flour (RCF). Regarding in vitro antihypertensive potential, germinated-extruded chia flour presented the best IC50 value. The main findings of this research show that extrusion processing applied in combination with germination is a promising strategy for increasing the nutritional value, bioactive compound content, antioxidant and antihypertensive potential, and microbiological stability of functional flours obtained from pseudocereal seeds.