There is an increased interest and need to make our economy more circular and our diets healthier and more sustainable. One way to achieve this is to develop upcycled foods that contain food industry by-products in their formulation. In this context, the aim of this study was to develop muffins containing upcycled sunflower flour (a by-product from the sunflower oil industry) and assess the effects of sunflower flour addition on the fibre, protein, amino acid, mineral content, and antioxidant activity measured by a Ferric Reducing Antioxidant Power (FRAP) assay and Photo chemiluminescence (PCL) assay. Results show that the sunflower flour inclusion significantly improved all the parameters analysed as part of this study. A more balanced muffin amino acid profile was achieved, thanks to the increased levels of lysine, threonine, and methionine, the limiting essential amino acids of wheat flour. We can conclude that upcycled ingredients, such as sunflower flour, could be used for the nutritional improvement of baked goods, such as muffins. Their addition can result in several nutritional advantages that could be communicated on packaging through the use of the appropriate EU nutrition claims, such as those on protein, fibre, and mineral content.