It remains unanswered how the light interacts with healthy and pathogen-infected onion tissues in a multi-layer structure. The overall goal of this study was to simulate light propagation (including scattering and absorption) in healthy and pathogen-infected onion bulbs in the visible and near infrared (NIR) range using Monte Carlo simulations. Healthy onions and bulbs infected with two major onion post-harvest diseases, Botritis Allii (Neck Rot) and Burkholderia Cepacia (Sour Skin), were considered as the subjects of the simulation. Multi-layered models (18 layers in total) of healthy and infected onion bulbs were developed representing onion structure in the form of parallel slabs. Variance of optical properties was introduced into the models using median and quartile values computed from the experimental data. Monte Carlo-simulations were performed for the developed models to generate optical responses of 33 cases of healthy and infected onions representing different stages of disease propagation in the spectral range 550-1650. nm. Optical responses of all the cases were assessed with statistical tests. Study of spatially-resolved scattering reflectance was conducted to identify patterns typical for infected onions. Optical responses were measured experimentally to validate the simulation results for healthy onions. A total of 18 configurations (out of 33) of infected onions showed significant difference from healthy bulbs and demonstrated great potential for nondestructive detection. Confident detection was determined for onions with infection as deep as in the 3rd scale. The proposed optimal window for disease detection was 670-870. nm. The greatest discrepancy between optical response of infected and healthy onions was found at 800. nm. Spatially-resolved reflectance of the Neck Rot-infected onions showed consistent lower intensity than that of healthy onions over the entire studied radial range, whereas the Sour Skin-infected onions exhibited differences in a limited radial range. Light penetration simulation revealed that photons can reach 5-6. mm deep in the bulb in the case of one dry skin in the wavelength of around 800. nm and 1100. nm. Validation results suggested that although the overall pattern of the simulated results and experimental measurements was similar, the systematic error was likely caused by the curvature of the onion bulb and the measurement instrument. This study was the first attempt to use Monte Carlo simulations in the field of post-harvest research to model complex tissues of vegetables using more than 2 layers. The results of the simulation could be useful in developing non-destructive optical sensing methods for onions.