Apple juice is a popular beverage worldwide, which is perceived as a wholesome and nutritious product. Overall quality of apple juice is an important factor to consider in processing, since some attributes, such as aroma, colour and flavour, are well appreciated by the final consumer, and are associated with freshness and authenticity. Non-thermal processing was tested in apple juice pasteurization in order to verify its feasibility in microbial inactivation, as well as its possibility of rendering a product impaired in terms of some sensory attributes. The non-thermal technique of high voltage pulsed electric fields (PEF) treatment, was compared with conventional high temperature-short time (HTST) pasteurization. Effects of process variables, such as voltage intensity and frequency for the PEF treatment, as well as temperature and time for the HTST pasteurization were investigated over inactivation of Escherichia coli and changes of pH and colour. Both techniques achieved more than five log reductions in microbial inactivation, normally considered the standard for fruit juices pasteurization. Apparently, PEF preserved better the pH than HTST as the thermal treatment showed an increase in this physicochemical property. Some variability was observed in terms of colour for all the treatments.