The aim of the present study was to evaluate the effectiveness of thermosonication (TS) as a conventional method on the physicochemical and microbiological quality of khoonphal juice to extend shelf life with retention of phytonutrients. The inactivation study of Escherichia coli (E. coli) and Saccharomyces cerevisiae (S. cerevisiae) was carried out through inoculation into the juice sample. pH and titratable acidity (TA) did not change significantly as a result of both the treatments. A slight decrease in total soluble solids was seen after pasteurization (PS). Thermosonicated juice showed a lesser total color difference and higher retention of bioactive compounds than PS juice. Both the treatments led up to 5 log cycles reduction of E. coli and S. cerevisiae and its survival curves were showed to be best fitted using the Weibull model with R2 value greater than 0.97 in all experiments. Thermosonicated juice had extended shelf life up to 10 days at 4°C with desirable physiochemical quality than conventional treatment. Practical applications Khoonphal juice is known to provide numerous health benefits but has a very less shelf life. Conventional methods which involve high heat treatment degrade the nutritional quality of the juice. Thermosonication is a process which not only improves the shelf life by reducing the microbial load but also protects the heat‐sensitive nutritional and bioactive compounds from degradation as it involves low temperatures. Thermal kinetics modeling of E. coli and S. cerevisiae in khoonphal juice can serve as a valuable tool in large scale production of khoonphal juice for planning the hazard analysis critical control points and make decisions as we can predict the expected changes that will occur in the microbial population during the process.

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