Jackfruit seed flour (JSF) and jackfruit seed starch (JSS) are utilized from agricultural by-products to take advantage of abundant raw materials. In this study, JSF and JSS were utilized to replace wheat flour in cookie products at various ratios of 10%, 20%, 30%, and 40%, and we assessed their effect cookies on nutritional quality, physicochemical properties, and sensory evaluation of the product. The results showed that JSF and JSS demonstrated significant potential in various cookie recipes. Jackfruit seed flour cookies (JSFCs), in particular, stood out due to their high nutritional content and exceptional physicochemical properties. On the other hand, results from sensory evaluation of jackfruit seed flour cookies (JSSCs) revealed they had a similar taste to wheat flour cookies (CCs) and were highly favored by participants. Notably, JSFCs exhibited a high fiber content of 4.67%, which indicates that JSF could provide numerous health benefits. Furthermore, JSFCs exhibited significantly higher polyphenol content and DPPH radical scavenging activity than JSSCs. The morphological properties of cookies and flours varied considerably among the products. This study supports sustainability by promoting eco-friendly ingredients, reducing the environmental impact compared to wheat flour. It also benefits local economies by repurposing overlooked jackfruit seeds as valuable raw materials, thus minimizing waste.