The importance of purple corn (Zea mays L.) varieties has increased due to their high anthocyanin contents both in the kernels and the degrained cob. The aim of this work was to separate anthocyanins from degrained purple-corn cobs to assess their pigmentation potential in food matrices. Two populations of purple corn were used, namely, Negro de Ixtenco (NIX) and Negro de Ixtenco x Negro de Perú (PIX), collected in Juchitepec, Mexico. Flours of degrained cob were obtained with average moisture, crude protein, ash, lipid, crude fiber, and carbohydrate contents of 7.06, 3.70, 4.48, 0.76, 37.73, and 46.27%, respectively. Aqueous biphasic systems composed of a mixture of 7.88% trisodium citrate, 2.63% citric acid, and 50.88% ethanol were applied at an atmospheric pressure of 77,993.0 Pa and 25 °C, aided by ultrasound and orbital agitation. Extracts with anthocyanin concentrations of 33.01 and 39.55 mg per gram of degrained corn cob were obtained from NIX and PIX, respectively. Pigmentation kinetics were assessed in yogurt and corn dough, which had a logarithmic tendency towards hue angles of 2.25 and 333.05°, respectively. A 60% pigmentation relative to the limit was suggested, which required 0.45 and 11.65% of the extract in yogurt and corn dough, respectively. Pigmentation stability was verified in refrigerated yogurt and in cooked corn dough.