AbstractDuring the last decade, consumers pay much attention to the food they eat. They try to choose functional products that have a beneficial effect on health and well‐being, beyond their typical nutritional function. For this reason, the primary aim of the study was to create a gluten‐free and dairy‐free cereal product with increased polyphenol and fiber content. Microencapsulation technology using freeze‐drying method and trehalose as matrix material was used in order to protect the polyphenols from the degradation during processing. The effect of the content of beta‐glucan concentrate, polyphenol microencapsulation and acai oil on the physicochemical properties of pastry products was studied. Response surface methodology was used to optimize the product formulation. The scope of work included analysis of process efficiency, instrumental analysis of color and texture, analysis of total antioxidant capacity, assessment of the content of polyphenols, flavonoids, and beta‐glucan, volume testing, analysis of the profile of fatty acids and volatile compounds, and assessment of sensory acceptability. Based on the obtained data, a response surface model was developed to determine the optimal recipe for the final product. The predicted data were verified using empirical methods. It was found that the optimal formulation of the product involves incorporating 6.48% polyphenol microcapsules, 7.60% beta‐glucan concentrate and 3.71% acai oil. The final product had higher content of polyphenols and beta‐glucan, as well as higher antioxidant activity compare to conventional product. Moreover, it was characterized by physical characteristics similar to the standard product and high sensory acceptability.Practical applicationsConsumers are currently eager to purchase fortified products with beneficial effects on health and well‐being. The developed functional product with increased polyphenol and beta‐glucan content, high antioxidant activity, is anticipated to garner significant consumer acceptance. The product, with its significant health‐promoting and well‐being enhancing properties, along with characteristics similar to conventional products, is poised to effectively meet consumers' needs and expectations. Additionally, it addresses a market void for bakery items tailored specifically for individuals with gluten intolerance, celiac disease, or cow's milk protein allergy. It provides a safe consumption option for these groups, offering a product similar to conventional items found on shelves that they are unable to consume.