Mild thermal treatment in combination with natural antimicrobials has been described as an alternative to conventional pasteurization to ensure fruit juices safety. However, to the best of our knowledge, no study has been undertaken to evaluate what could be its effect on their color and nutritional value. This study therefore aimed at assessing how a low thermal pasteurization in combination with carvacrol could affect these parameters, with orange, pineapple, and watermelon juices as selected fruit juices. The experimental design used had levels ranging from 50 to 90°C, 0 to 60 μl/L, and 0 to 40 min for temperature, concentration of carvacrol supplemented, and treatment length, respectively. The only supplementation of fruit juices with carvacrol did not affect their color. In comparison with high thermal pasteurization (>70°C), a combined treatment at mild temperatures (50–70°C) better preserved their color, antioxidant capacity (AOC), and vitamin C content, and increased their total phenolic content (TPC). Globally, carvacrol supplementation had a positive impact on the TPC of thermally treated juices and increased the AOC of treated watermelon juice, which was the lowest of the three fruit juices. Mild heat treatment in combination with natural antimicrobials like carvacrol is therefore an alternative to limit the negative effects of conventional pasteurization on fruit juices quality.