Potatoes inoculated withPectobacterium carotovorumspp.,Aspergillus flavusandAspergillus niger, along with healthy (control) samples, were stored at different storage temperatures (4 ± 1 °C, 8 ± 1 °C, 25 ± 1 °C) for three weeks. Volatile organic compounds (VOCs) were mapped using the headspace gas analysis through solid phase micro extraction–gas chromatography–mass spectroscopy every week. The VOC data were arranged into different groups and classified using principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA) models. Based on a variable importance in projection (VIP) score > 2 and the heat map, prominent VOCs were identified as 1-butanol and 1-hexanol, which can act as biomarkers forPectobacterrelated bacterial spoilage during storage of potatoes in different conditions. Meanwhile, hexadecanoic acid and acetic acid were signature VOCs forA. flavus, and hexadecane, undecane, tetracosane, octadecanoic acid, tridecene and undecene were associated withA. niger. The PLS-DA model performed better at classifying the VOCs of the three different species of infection and the control sample compared to PCA, with high values of R2(96–99%) and Q2(0.18–0.65). The model was also found to be reliable for predictability during random permutation test-based validation. This approach can be adopted for fast and accurate diagnosis of pathogenic invasion of potatoes during storage.