Quinoa plants, originating from the Andean mountains in South America, have a large scale of biological diversity. Along with the cultivation favorableness of quinoa, it reveals superior nutrition aspects. In comparison with cereal crops, like rice, maize, and wheat, quinoa seeds contain valuable quantities of the protein of remarkable quality. The current study compared four quinoa cultivars from different origins in terms of protein composition and germinability. In addition, this study focused on the effect of different geographical cultivation areas on the protein composition of wild Egyptian quinoa seeds and three other cultivars that vary in their cultivation origins. Significant differences were observed among the quinoa varieties in the germination percentage (GP), shoot length (SL), and root length (RL). Using the technology of Near-InfraRed Spectroscopy, the highest protein value was recorded for the American variety (18.39%), followed by the Wild Egyptian variety (17.16%). The aromatic phenylalanine recorded the highest concentration of the essential amino acid bulk. The Rainbow variety contained 12.7 g-aa/kg protein, followed by the wild Egyptian variety with 4.9 g-aa/kg protein. In turn, glutamic was the most abundant amino acid of the non-essential amino acids, with 10.1, 4, 23.4, and 4 (g-aa/kg protein) for quinoa varieties, Wild Egyptian, American, Rainbow, Black, respectively. SDS-PAGE was used to identify the allelic variations in the seed storage protein profiles among the studied quinoa varieties. The studied quinoa varieties showed 23.81% of the polymorphism in the protein bands, with a mean band frequency of 0.881. The resulting protein bands fluctuated in the range between 115.02 and 16 kDa. With a similarity percentage (90%), Wild Egyptian and the Rainbow quinoa varieties can be classified in one clade.