The purpose of this study was to investigate the effect of non-thermal technology, high power ultrasound (HPU) on inactivation of Aspergillus ochraceus 318, Penicillium expansum 565, Rhodotorula sp. 74, Saccharomyces cerevisiae 5 and Alicyclobacillus acidoterrestris DSM 3922 in clear juices and nectars from apple, blueberry and cranberry juice concentrate. Inoculated juice and nectars were treated by high power ultrasound (20 kHz) according to procedure set by central composite design (CCD). Three operational parameters, amplitude (60, 90 and 120 μm), temperature (20, 40 and 60 °C), and treatment time (3, 6 or 9 min) were varied in order to observe the influence of ultrasound and combination of ultrasound and slight heating (thermosonication) on growth and inactivation of selected microorganisms. Number of vegetative cells of A. acidoterrestris DSM 3922 were not significantly reduced by high power ultrasound (p > 0.05), except in apple juice, where statistical significant (p < 0.05) influence of quadratic interaction of amplitude on bacteria reduction were observed. In all samples of fruit juices and nectars in terms of ultrasonic treatment at 60 °C and times of 3, 6 and 9 min, regardless of the value of the amplitude, complete inactivation of the growth of yeasts and moulds were achieved, while at 20 and 40 °C it is not observed. The value of reduction of cells of selected yeasts and moulds for ultrasound treatments at 60 °C and the duration of the 3, 6 and 9 min ranged from 3.556 to 5.934 log units, depending on the initial number of selected yeasts and moulds before treatment.