The aim of the study was to evaluate the functional properties of muffins fortified with white clover flowers (Trifolium repens L.), which were added to the dough in the following amounts: (i) 0% (control); (ii) 2.5%; (iii) 5.5%; (iv) 7.5%; and (v) 10%. The organoleptic properties were assessed by a panel of consumers. Additionally, the following parameters were also tested: basic chemical composition, total polyphenols, the antioxidant activity together with antiproliferative effects on the A375 melanoma cell line, starch nutritional fractions and the in vitro glycemic index. As a result, replacing wheat flour with white clover flour significantly affected the color, aroma and taste of the muffins. The content of proteins, fats, total ash, dietary fiber, resistant starch (RS), slowly digestible starch (SDS),total polyphenols and antioxidant activity increased statistically significantly with the elevated amount of white clover flour added to the dough. At the same time, the content of free glucose (FG), rapidly available glucose (RAG) and rapidly digestible starch (RDS), the value of the in vitro glycemic index and the viability of melanoma cancer cells decreased significantly. The muffins enriched with white clover flowers might constitute an interesting proposition and extension of the existing assortment of confectionery products.