Apple juice is one of the most consumed fruit juices in the world. Raw apple juice is viscous, turbid, and brown in color and contains several spoilage microorganisms. These are the reasons behind the application of several steps of clarification and stabilization prior to juice commercialization. Thermal pasteurization remains the most used process for apple juice microbial stabilization, but it damages its organoleptic and nutritional characteristics. Juice settling used for clarification does not allow the achievement of the desired level of clarification. Therefore, this article provides a comprehensive and bibliometric review of all the alternative treatments for thermal pasteurization in order to reduce microorganisms and patulin levels such as pulsed electric fields, microwave processing, high hydrostatic pressure, ultrasonication, etc., and their effect on apple juice characteristics as well as the techniques used for apple juice clarification.