This research focuses on the development of functional gluten-free breads with the use of pseudocereal, Psyllium and gluten-free sourdough to replace commercial yeast, fortifying them with non-encapsulated spirulina (NES) and encapsulated spirulina (ES). For that, different gluten-free breads were made with sourdough: three control breads differentiated by sourdough (quinoa, amaranth and brown rice), three free spirulina-enriched breads differentiated by sourdough, the other three breads enriched with encapsulated spirulina and a gluten-free commercial bread (COM). Antioxidant capacity, phenolic compounds, nutritional composition, physico-chemical parameters (color, pH and acidity), folate content, amino acid profile, reducing sugars, mineral composition, mineral bioaccessibility, fatty acid profile and sensory acceptability were evaluated. Free spirulina increased the nutritional properties of the bread, increasing the content of protein, total folate, 9t, 11t-C18:2 (CLA), C22:6n-3 (DHA), minerals and decreasing the carbohydrate content. However, encapsulated spirulina increased sensory properties, antioxidant capacity, phenolic compounds, bioaccessibility of iron and amino acids. The results have demonstrated the important potential of the use of bread as a means to combat nutritional deficiencies in celiacs, promoting the use of spirulina in bread within the healthy food market and the use of encapsulated spirulina protecting the antioxidant potential of spirulina, representing an alternative for the baking industry. •Development of encapsulated Spirulina and its application in a bakery product.•Bread reformulated: good sensory acceptance and retained the bioactive after the thermal process.•The encapsulation of Spirulina reported bioactive compounds in bread.•Development of clean-label bakery and the replacement of wheat and gluten with others cereals.