The present study aimed to investigate the effect of recipe and temperature–time on the formation of acrylamide and 5-hydroxymethylfurfural (HMF) during biscuit baking. Baking experiments were performed with biscuits of two different recipes, with and without NaCl, at 180 °C, 190 °C and 200 °C. Acrylamide and HMF reached highest concentrations at 200 °C for both recipes. The presence of NaCl in the biscuit formulation lowered acrylamide concentrations at 180 °C and 190 °C but not at 200 °C, and led to higher concentrations of HMF at all the tested temperatures. Sucrose hydrolysis was a key step in acrylamide and HMF formation during biscuit baking, even though a significant amount of acrylamide already had formed before the onset of sucrose hydrolysis. A lag phase was observed before sucrose hydrolysis occurred, which might depend on the melting of crystalline sucrose occurring at approximately 180 °C. A mathematical model based on the chemical reaction pathways was developed for the recipe with NaCl baked at 200 °C. The model described the chemical evolution during the last part of biscuit baking, and accurately predicted acrylamide and HMF content at the end of baking. The model showed the significant contribution of the reducing sugars to the formation of both acrylamide and HMF. The model could not be extended to the entire baking period because it was not possible to incorporate the lag phase observed before sucrose hydrolysis. The results reported in this study confirm that the kinetics of acrylamide and HMF formation in real food and dry systems may depend on the physical state of their precursors.