The increase of people suffering from celiac disease, and dietary fiber deficiency has become an issue that needs extra attention by people around the world. This research was aimed to study the gluten-free cookies incorporated with different seed flours as dietary fiber source. The effect of different blanching methods on the fruit seed flours yield and lightness was examined. The effect of the ratios of different fruit seed flour to tapioca flour and gelatinization states of tapioca flour on cookies was evaluated based on the panel acceptance, chemical, and physical characteristics. Results showed that the blanching method affected the yield and lightness of the seed flours. The best treatment for the chempedak seed was water-blanching for 20 min; for the jackfruit seed was water-blanching for 20 min; for durian seed was steam-blanching for 10 min. The results showed that the fruit seed flour to tapioca flour ratios and gelatinization state affected all cookie parameters including diameter increase, spread ratio, yield, color, moisture content, hardness, as well as the aroma, color, taste, texture, and overall acceptance. Based on the panel acceptance, the most accepted cookies was made from the combination of chempedak seed flour and gelatinized tapioca flour with 40:60 ratio; chempedak seed flour and non-gelatinized tapioca flour with 40:60 ratio. The most accepted jackfruit seed flour cookies were made from combinations of jackfruit seed flour with non-gelatinized tapioca flour with ratio of 20:80; jackfruit seed flour and gelatinized tapioca flour with ratio of 20:80. For the most accepted durian seed flour cookies were made from the combinations of durian seed flour and non-gelatinized tapioca flour with ratio of 20:80; durian seed flour and non-gelatinized tapioca flour with ratio of 40:60. The jackfruit seed flour and non-gelatinized tapioca flour of 20:80 ratio cookie contained 5.34±0.06% dietary fiber, while chempedak seed flour and gelatinized tapioca flour of 40:60 ratio contained 7.68±0.57%, and durian seed flour and non-gelatinized tapioca flour of 20:80 ratio contained 4.38±0.20%. Hence, the gluten-free cookies were successfully prepared and may serve as a source of dietary fiber; and since it is gluten-free, it is good for people with celiac disease.