Juices have lower quantities of total phenolics content (TPC), anthocyanins, and antioxidant compared to the whole fruit. Furthermore, only low levels of these compounds are extracted from fruit skins during the initial juice processing steps with the majority staying in the skins and seeds. Once the initial juicing starts, degradative reactions begin to convert endogenous polyphenols into new compounds. Even though temperature is the key factor which determines this degradation rate, there is limited information about the temperature at which it begins, and the effects of centrifuging particles before or after thermal processing. The objectives were, first to determine the effects of different time–temperature conditions on the TPC, and antioxidant activity; second, to assess both parameters when the juice was clarified before or after thermal processing. Processing conditions were: 50–80 °C, and 1–30 min as residence time. At temperatures greater than 60 °C, both parameters began to decrease. The optimum processing condition for greatest retention of both parameters was 60 °C and 30 min. TPC and antioxidant activity retention were significantly higher on the juice clarified after thermal processing, compared to the one clarified before. This information can help juice processors and equipment manufacturers to optimize their process and design.