Fresh onions are dehydrated to increase their shelf-life. Primarily, open dehydration techniques like solar dehydration come with the problem of contamination through natural air convection. A solar conduction dryer that uses conduction, convection, and radiation for dehydration of food samples is exploited in this study. The food samples are often contaminated by Bacillus and Aspergillus species spores. As a remedy, pulsed light treatment as a non-thermal technology and infrared treatment as a thermal technology are studied and compared. Bacillus cereus and Aspergillus niger spores are chosen as a representative of bacterial and fungal contamination in onions. Dehydrated onion shreds with varying water activities (0.4, 0.5, 0.6) were treated. The spore inactivation was best described by Weibull model as compared with first-order model. Scanning electron microscopy images of the microbial cells showed surface distortions on the bacterial and fungal spores. The effect of the treatment technologies on the colour, flavour (thiosulphinate and pyruvic acid concentration), total phenolic and flavonoid content, and ascorbic acid concentration are compared. Overall, pulsed light treatment showed promising inactivation with a maximum log reduction of 4.5 log B. cereus spores·g−1 and 3.1 log A. niger spores·g−1 at 2.131 J·cm−2 in samples with water activity 0.6. The inactivation rate increased with an increase in water activity. The colour was better retained in pulsed light treated samples. The thiosulphinate content (9.24 μmol·g−1), total phenolics (0.268 mg GAE·g−1), and flavonoid content (0.344 mg QE·g−1) in the sample were improved upon pulsed light exposure.Graphical