<p>This research evaluated how both the maize alkaline cooking processes (traditional and extrusion-based nixtamalization) and tortilla baking step affect the chemical composition, physicochemical parameters, antioxidant activity, and phytochemical compounds in tortillas made from QPM. While the chemical composition of QPM was largely unaffected by the alkaline processing methods, extrusion-based nixtamalization exhibited a higher retention of total phenolic compounds (94% retention compared to 72% in the traditional nixtamalization process), and antioxidant activity (87–98% retention compared to 56–66% in the traditional nixtamalization process by ABTS, DPPH, and FRAP methods). Furthermore, alkaline extrusion led to higher melanoidin formation, compounds associated with antioxidant properties. Nevertheless, the tortilla baking step slightly reduced lipid content, it did not significantly alter (chemical composition, total phenolic content, and antioxidant activity) the other key nutritional and functional properties. Although the subsequent baking step slightly reduced the melanoidin content initially formed during both nixtamalization processes, the overall melanoidin content in the final extruded tortilla remained higher than in the traditional nixtamalized one. This was supported by the observed color darkening (reduction in Hunter L value and increase in ΔE), which is indicative of Maillard reaction products, including melanoidins. These findings support the potential of extrusion processing as a more sustainable and health-promoting method for producing QPM-based tortillas.</p>