The lime-cooking extrusion represents an alternative technology for manufacturing pre-gelatinized flours for tortillas with the advantages of saving energy and generation of null effluents. The phytochemical profiles (total phenolics, anthocyanins) and antioxidant activity of four different types of whole pigmented Mexican maize [white (WM), yellow (YM), red (RM), blue maize (BM)] processed into tortillas were studied. The lime-cooking extrusion process caused a significant decrease (p < 0.05) in total phenolics and antioxidant capacity when compared to raw kernels. Most of the total phenols assayed in raw grains (76.1-84.4 %) were bound. Tortillas from extruded maize flours retained 76.4-87.5 % of total phenolics originally found in raw grains. The BM had the highest anthocyanin content (27.52 mg cyanidin 3-glucoside/100 g DW). The WM, YM, RM and NWM contained 3.3, 3.4, 2.9, and 2.2 %, respectively, of the amount of anthocyanins found in BM. The BM lost 53.5 % of total anthocyanins when processed into extruded tortillas. Approximately 64.7 to 74.5 % of bound phytochemicals from raw kernels were the primary contributors to the ORAC values. Extruded tortillas retained amongst 87.2 to 90.7 % of total hydrophilic antioxidant activity when compared to raw kernels. Compared to the data reported by other authors using the conventional process, the lime-cooking extrusion process allowed the retention of more phenolics and antioxidant compounds in all tortillas.