Centrifugation is a technique applied to assist in the freeze concentration of fruit juices and solutions. The aim of this work was to study the influence of the time–temperature parameters on the centrifugation process as a technique applied to assist in the first cycle of the freeze concentration of blueberry juice. A completely randomized 4 × 3 factorial design was performed using temperature and time as the factors, and the response variables included the percentage of concentrate, efficiency and solutes recovered. The results were evaluated using multiple linear regression, random forest regression, and Gaussian processes. The solid content in the concentrate doubled compared to the initial sample (18 °Brix) and approached 60% in the first cycle of blueberry juice freeze concentration. The combination of factors affected the percentage of the concentrate and solutes recovered, and the optimum of concentration was obtained at 15 °C with a centrifugation time of 20 min. Gaussian processes are suggested as suitable machine learning techniques for modelling the quantitative effect of the relevant factors in the centrifugation process.