The stability of free tryptophan (Trp) was examined in five cookie-resembling models at varying baking temperatures and durations. Trp was measured by HPLC coupled with a fluorescent detector. Trp degradation was significantly greater in cookies formulated with glucose compared with sucrose, regardless of the temperatures and durations of baking. A lag period was clearly observed in cookies formulated with sucrose. The type of sugar used in the dough formulation affected not only the thermal destruction kinetics but also the degree of degradation of free Trp. However, the type of leavening agent (ammonium bicarbonate versus sodium bicarbonate) did not affect the rate of Trp destruction as happens in Maillard-driven reactions. In addition, the free Trp content was analyzed in nine different flours and sixty-two commercial cookies, and it was found that free Trp varied from 0.4 to 1287.9 mg/kg for rice and wheat bran, respectively. It was found that free Trp was significantly higher in dietetic commercial samples formulated with wheat bran compared with other flours.