This study aimed to develop gluten-free biscuits with enhanced nutritional value and taste, while reducing high-calorie ingredients, particularly sugar. Two formulations have been devised to create biscuits customized for people with gluten allergies. Corn flour has been replaced with chickpea flour at a consistent rate of 20% to boost nutritional value with its high protein content. Furthermore, quinoa flour (QF) has been added in different quantities (20%–40%) for its protein richness (14.87%) and amino acid content. Another option suggests using Jerusalem artichoke (JAF) flour, used as a sugar substitute, as it is known for its health benefits and high inulin content. It has been integrated into biscuit formulations at levels from 20% and 40%. Both formulations have also undergone a reduction in sugar content of 15% and 30%. The chemical properties and phytochemical content of the raw materials were evaluated. Jerusalem artichoke flour (JAF) exhibited the highest antioxidant activity (92.02%). The addition of QF to biscuits increased protein content with higher replacement rates, as well as fiber content and mineral levels. JAF was thoroughly examined in two specific formulations as a partial sugar substitute. The inclusion of JAF caused minimal changes in physical properties, and sensory evaluations indicated satisfactory results, especially for biscuits containing up to 40% QF. Furthermore, incorporating 20% JAF allowed for a 30% sugar reduction without affecting flavor. Additionally, the QF-containing supplemented biscuits had a reasonably high essential amino acid balance, indicating that they may help children with celiac disease consume more amino acids.