A high-fidelity coagulation driven kinetic Monte Carlo (KMC) model is developed to study the physics of the nonlinear interplay between competing exothermic collision-coalescence mediated surface oxidation and complex morphologies in aggregated nanostructures generated during gas-phase synthesis of nanoparticles. Results suggest a twofold oxidation mechanism in which thermally activated processes form a critical oxide shell, beyond which morphological complexity of nanoparticles gives rise to enhanced oxidation. Simulation results for the example case-study of Al nanoparticle synthesis in air under different prototypical processing conditions, i.e., temperature, pressure and volume loading, show the efficacy of the model in determining optimal process variables for tuning the structural and chemical makeup of energetic nanomaterials. Finally, it is demonstrated that inclusion of nonisothermal coalescence that leads to the formation of fractal-like nanoparticles (particularly, < 15 nm) gives rise to higher degrees of oxidation when compared to instantly coalescing spherical particles. (c) 2012 American Institute of Chemical Engineers AIChE J, 2012