Consumers have given preferences to food products that, in addition to the nutritional properties, also present bioactive characteristics with beneficial health effects. The use of Nonconventional Food Plants (NCFP) has been an asset for the food industry, not only due to its abundance but, also, because it does not compete with other vegetable matrices used for human consumption for its nutritional properties, chemical and bioactive potentiality. The present work aimed to study the granulometry and water absorption index of three seeds of unconventional food plants: niger, millet and birdseed, followed by their nutritional value, content in free sugars, fatty acids, organic acids, tocopherols and phenolic compounds by chromatographic methods and, also, the evaluation of the antioxidant, hepatotoxic and antimicrobial potential in their hydroethanolic extracts. Bakery products were developed with a partial replacement of wheat flour, using the centroid simplex method to understand the effect of applying NCFP flours in the final physical–chemical characteristics. The high granulometry associated with the high water absorption index indicates that the use of NCFP flours would have to be complemented with other flours for baking. The chemical composition of niger seed stood out the most; however, all seeds presented relatively low IC50 and MIC values for the inhibition of lipid peroxidation and antimicrobial activity, respectively. Finally, breads made with a mixture of millet and birdseed flour showed the greatest similarity to the control bread. Considering their composition in bioactive compounds, the use of these seeds is highly advisable in the context of a fortified diet, being sources of compounds of high nutritional value and with beneficial health effects for the final consumer.