The present research sought to evaluate the detection capacity of the electronic nose for the hazelnut aroma in a filled chocolate wafer, measuring its release and physical–chemical, thermal, and microbiological properties during 60 days where the product was stored at 25 °C and 40 °C. It was found that moisture, Aw, pH, thermal resistivity, and diffusivity remained stable during storage at both temperatures, with no significant difference (p > 0.05). While there was variation in color (L*, a*, b*, and ΔE) and in thermal conductivity. The microbiological analyses of mesophilic bacteria, Escherichia coli, Salmonella spp., and coagulase-positive staphylococci were maintained in accordance with the standards established by current legislation. The results obtained with the sensors array showed good sensitivity and a high limit of detection (> 0.001 mg/mL) for hazelnut aroma. The electronic nose was able to discriminate between the release of volatiles from chocolates stored at 25 and 40 °C, with a greater response observed at high temperature (40 °C) at the beginning of storage. Through the application of the Arrhenius model, we successfully determined the activation energy for key color components (L*, a*, b*) and thermal conductivity. Additionally, our findings revealed a good fit of volatile component release to the zero-order model, characterized by a high correlation coefficient (> 0.9). These findings underscore the importance of considering storage temperature when preserving the quality of products such as chocolates. Furthermore, the study validates the use of the electronic nose as a viable technique for analyzing volatiles in food, providing valuable insights for the food industry.