Germination and extrusion are two processes that could affect beany flavors in pulse-based high-moisture meat analogs (HMMAs). This research studied the sensory profile of HMMAs made by protein-rich flours from germinated/ungerminated pea and lentil. Air-classified pulse protein-rich fractions were processed into HMMAs with twin screw extrusion cooking, optimized at 140 °C (zone 5 temperature) and 800 rpm screw speed. Overall, 30 volatile compounds were identified by Gas Chromatography-Mass Spectrometry/Olfactory. Chemometric analysis exhibited that the extrusion markedly (p < 0.05) reduced beany flavor. A synergistic effect of germination and extrusion process was observed, decreasing some beany flavors such as 1-octen-3-ol and 2,4-decadienal, and the overall beany taste. Pea-based HMMAs are suitable for lighter, softer poultry meat, while lentil-based HMMAs are suited for darker, harder livestock meat. Those findings offer novel insights into the regulation of beany flavors, odor notes, color, and taste to improve the sensory quality of HMMAs.