This paper presents the results of a study on the influence of juice extraction and thermosonication methods on the content of microorganisms in juices stored under refrigeration and in ambient temperature. It was determined that the type of extraction device used influenced the content of microorganisms in juice. The lowest total content of mesophilic microorganisms was obtained in juice extracted on a piston press, and the highest was obtained using a centrifuge. The additional purpose was to evaluate the influence of ultrasonic treatment on selected parameters of apple juice quality: cloud value, antioxidant activity, total phenolic content, flavonoid content, and anthocyanin content. The ultrasound treatment of juice from the piston press was conducted at two levels of radiated sonic power so as to obtain sublethal and lethal temperatures of the juice. It was demonstrated that only ultrasound treatment within the range of lethal temperatures was sufficient to deactivate microorganisms. It was determined that thermosonication did not influence the deterioration of chemical properties of juices, with the exception of decreased anthocyanin content. The described method enables prolongation of the shelf life of fresh apple juice under refrigeration to 168 hours (7 days).