The aim of this study was utilization of various seed flours on cake making and to investigate the effect on dough rheology. Apricot seed flour, sour cherry seed flour, pomegranate seed flour, and pumpkin seed flour were used at 5%, 10% and 15% substitution levels to wheat flour. Extensograph and Mixolab were used to determine the rheological and techno-functional attributes of wheat flour substituted with seed flours. Cake quality was investigated in terms of volume, baking loss, hardness, elasticity and sensorial properties. Apricot seed flour substitution highly affected the energy and maximum resistance. Pumpkin seed flour showed a higher effect on extensibility and Mixolab parameters than other seed flours did. Sensorial analysis showed that 5% substitution level was acceptable, however the substitution at 15% level caused a high negative impact on sensorial properties. It was shown that some Mixolab parameters could be used as indicators for the cake quality. The overall results indicated that rheological properties of wheat flour are affected based on the substitution level and it is possible to produce cakes with improved quality attributes with an adjustment of substitution level. The results could have important implications for the valorization of seed flours to produce functional baked products having high protein content.