There is an increasing demand from the food industry for complex products with controlled nutritional and sensorial properties (vitamins, antioxidants or flavour compounds contents). Many of these properties result from chemical reactions induced in food by the technological treatments. The conception of foods and the reappraisal of the products and processes require strategies allowing the appearance and the protection of valuable compounds to be controlled. The reactions in a food system are described as a complex network of many chemical reactions. But only a small part of all the molecules consumed or synthesized by these reactions can be experimentally observed. A major stake of this study was to propose a methodology to extract a simplified (so-called apparent) identifiable reaction pathway which could give a reliable representation of the complex reaction system occurring during cooking of a bakery product. Such a methodology was based on theoretical knowledge of the system, taking into account the experimental constraints and the available information. A limited number of observable chemical markers were selected according to their ability to point out different advancement steps of the reactions (Maillard reaction, caramelization, lipid oxidation). The use of statistical methods made it possible to extract an apparent reaction pathway from available information. The representation of the reaction system as a stoichio-kinetic model, combined with mass balance and enthalpy equations, can provide a better knowledge of the transfer-reaction coupling and its consequences on the final products characteristics.