Maize represents one of the most important staple crops in the Peruvian highlands. The abundant morphological diversity found in Peruvian maize from the highlands was classified by a previous published work into six groups: (i) primitive races—PRs, (ii) anciently derived or primary races—ADPRs, (iii) lately derived or secondary races—LDSRs, (iv) introduced races—INTRs, (v) incipient races—INCRs, and (vi) imperfectly defined races—IDRs. To date, Peruvian maize races have not been further examined. Here, we conducted multivariate analyses using the publicly available dataset of 124 morphological quantitative characters (ear, plant, leaf, tassel, pericarp, cob, endosperm, and kernel) for 43 Peruvian maize races scored to classify them in an attempt to provide additional evidence for that grouping and for determining congruence with our molecular study. Principal component analysis demonstrated that the first two components (CP1 and CP2) summarized 23.03% of the total variance. The top three variables that contributed more to CP1 were the leaf width, tassel length of the branching space, and tassel number of the primary branches, while the ear diameter base, ear internal diameter, and ear cupule width contributed more to CP2. Principal component analysis grouped all primitive races. The other races did not show a consistent clustering. On the other hand, most of the LDSR, INT, INCR, and IDR groups formed a single group. Our hierarchical clustering analysis using the average method grouped all PRs, except Kculli, in a single clade. In addition, most of the ADPRs were grouped in two clusters. These results are in partial agreement with our molecular work. Further research is needed to determine the phenotypic plasticity of the races of Peruvian maize, considering that these landraces are in constant evolution in the Andes. We expect our work will stimulate other researchers to conduct maize germplasm characterization. We aim to use this precious genetic resource to alleviate poverty in the Peruvian Andes.