The transformation of renewable feedstocks into aromatic chemicals holds immense potential for advancing a green, low-carbon economy and fostering sustainable development. Herein, we present a novel approach for the conversion of isoeugenol, a renewable lignin derivative, into the valuable flavoring agent vanillin, utilizing ozone as an environmentally benign oxidant. The process optimization was significantly enhanced by the integration of in situ Attenuated Total Reflectance Infrared (ATR-IR) monitoring. The introduction of H2O not only accelerated the decay of carbonyl oxides (Criegee intermediates) but also mitigated safety hazards stemming from the vigorous decomposition and heat release of secondary ozonides. Compared to the conventional Thin Layer Chromatography (TLC) method, ATR-IR monitoring demonstrated superior sensitivity and precision in determining the reaction endpoint, leading to a remarkable vanillin yield of 96.86% upon complete conversion of isoeugenol. Additionally, a comparative assessment of the sustainability of our approach with existing methods was undertaken, and valuable recommendations for safety assessments were provided to ensure the inherent safety of chemical engineering reactions. The present study serves as a pioneering effort in facilitating the implementation of a scalable, economically feasible and environmentally sustainable strategy for biomass flavor production, while contributing to the broader adoption of in situ spectroscopic technology within the larger economy.