Maize is one of the most important staple crops in the highlands of the Andean region of Ecuador, Peru, and Bolivia. Most seeds come from landraces, with their own kernel characteristics. The kernels are used for the elaboration of traditional dishes and other elaborates for human consumption. In this region, maize breeding is conducted mainly by public institutions. In this review, we outline the methodology that has been used by the maize breeding programs (MBPs) of the National Institutes for Agricultural Research and other institutions in the highlands of Ecuador, Peru, and Bolivia during the last 20 years. The main objective of MBPs in the region has been to develop more uniform and productive open-pollinated varieties (OPVs) of floury maize (Zea mays L. var. Amylacea), which is the most important type of maize in the area. Participatory plant breeding, combined with half-sib, has been used to breed new maize varieties. At least 18 OPVs of floury maize have been released into the Andean region in the last 20 years. Breeding this type of maize has been very important to conserve diversity and promote consumption in the region, but they have had very little impact on yield. The yield of floury maize is around three times below that of dent or semident maize grown in the region. Therefore, there is a need to apply new breeding techniques in the region to accelerate the development of more productive floury-maize cultivars.