This study aimed to evaluate different methods to produce flour from tilapia carcasses (cooked, cooked/aromatized, and flavored), and the use of different concentrations of cooked tilapia carcass flour for the enrichment of tapioca cookies. Tapioca cookies with the inclusion of cooked carcass flour from different fish species (tilapia, tuna, sardines, and salmon) were also studied. The flour from the cooked carcass showed low moisture and lipid contents and high protein, calcium, and phosphorus contents, as well as high L* values, and low a* and b* values. The tapioca cookies enriched with cooked tilapia carcass flour (9%) showed high protein content and good sensory acceptance. Concerning the cookies made with flour from different fish species, the tilapia flour led to an increase in protein contents, as well as linoleic, arachidonic, and eicosapentaenoic fatty acids concentrations of the cookies. These cookies also received the highest purchase intent scores. Therefore, the inclusion of flour from fish carcasses in tapioca cookies may be an effective alternative to increase the nutritional value of the product, besides adding value to the fishery waste and reducing the environmental impact of farming fish.