In the present investigation, the treatment of amoxicillin (AMX)-polluted water by the activated persulfate (PS) was considered. As a novel research, continuously electro-generated magnetite (Fe3O4) nanoparticles (CEMNPs) were utilized as the activator of PS in an electrochemical medium. The PS/CEMNPs displayed a remarkable enhancement in the decomposition of AMX molecules up to 72.6% compared with lonely PS (24.8%) and CEMNPs (13.4%). On the basis of pseudo-first order reaction rate constants, the synergy percent of about 70% was achieved due to the combination of PS with CEMNPs. The adverse influence of free radical-scavenging compounds on the efficiency of the PS/CEMNPs process was in the following order: carbonate < chloride < tert-butyl alcohol < ethanol. Overall, these results proved the main role of free radical species in degrading AMX. The implementation of ultrasound (US) enhanced the performance of the PS/CEMNPs process. Nevertheless, the highest degradation efficiency of about 94% was achieved when UV254 lamp was joined the PS/CEMNPs system. Under UV254 and US irradiation, the results showed significant potential of the PS/CEMNPs process for degrading AMX antibiotic and generating low toxic effluent based on the activated sludge inhibition test. However, more time is needed to achieve the acceptable mineralization.