The article presents the results obtained through an advanced modeling of fast developing processes, such as oxidation reactions applied to biomass products, which are useful to quantify the evolution of the reactants and the reaction products throughout the entire process. The model enables the real time observation of the process, starting with process initiation, run, and burnout, providing useful information for transitory regimes when the experimental measurements and continuous observation are very difficult due to sampling and analyzing equipment limitation. The modeling tool used within this study is based on bond graph methodology, which is an alternative to classic modeling methods. This tool integrates advanced chemical dynamics information (reaction kinetics, formation enthalpy, mass, and energy balance) delivering results for fast reacting chemical systems. The results present the evolution of reaction products concentration during the reaction start-up according to the time period imposed by the user. The article highlights the importance of accurate modeling of transitory regimes of the processes when the concentration of the pollutants emissions is at the highest peak, providing information for processes control and optimization.