The increasing interest in quinoa in Europe has generated a large number of studies with this seed as a partial substitute for refined wheat flour in bakery products as a strategy to improve their nutritional value. However, the wide genetic diversity of this seed offers very different compositions in different varieties, which would lead to different technological behaviours in the breadmaking process. The aim of this work was to make a comparative study of the protein profile and rheological and thermal properties of three varieties of quinoa widely available commercially in Europe to study their technological potential as breadmaking ingredients with 25% replacement of wheat flour by whole quinoa flour. The results obtained during the analysis offered a view of the proteins present in the various quinoas, and of the processes of hydrolysis and generation of new bonds between wheat and quinoa proteins during the breadmaking process. The changes in the thermal and pasting properties of the bread doughs that included whole quinoa flour led to the development of baked products with different physico-chemical and textural properties, producing an increase on crumb staling. However, replacement of 25% of the wheat flour with whole quinoa flour produced only a slight decrease in the technological quality of the products. A significant increase (p < 0.05) in dietary fibre, minerals, lipids, and proteins in comparison with a whole wheat product, together with the overall consumer acceptance of the products that were developed, was conclusive for proposing replacement with quinoa flour as a strategy for nutritional improvement in the manufacture of bakery products.