The effects of four important stages of pomegranate juice processing, i.e., pasteurization, enzymatic treatment, filtration and thermal concentration were evaluated based on physicochemical characteristics, bioactive compounds (phenols, flavonoids and anthocyanins) and antioxidant activity (DPPH, FRAP and CUPRAC). Pasteurization had no significant effect on total phenolic content, but it significantly reduced the total flavonoid and total anthocyanin contents. Enzymatic treatment, filtration and thermal concentration significantly reduced the total phenolic and total flavonoid contents. Pasteurization and thermal concentration had no significant effect on FRAP and CUPRAC values. The IC50 value increased notably during enzymatic treatment, filtration and thermal concentration. Processing the pomegranate juice and the subsequent production of pomegranate concentrate led to an overall reduction of total phenolic content, total flavonoid and total anthocyanin contents by 68, 46 and 61%, respectively. Moreover, the processing caused reductions in total antioxidant capacity by 27 and 9%, determined via the CUPRAC and FRAP methods, respectively.