Vacuum freeze-drying as a process for achieving high product quality has attracted increasing attention in the last decade. Particularly in the pharmaceutical field and food processing industries, lyophilization can produce high-quality products compared to samples dried by conventional methods. Despite its benefits, lyophilization is a time-consuming and costly process that requires optimization of a number of process parameters, including shelf temperature, chamber pressure, freezing rate, and process time. This paper reports on the implementation of heat flux measurements that allow noninvasive real-time determination of the endpoint of the primary drying stage as an essential parameter for the effective optimization of the overall drying time. Quantitative analysis of the drying kinetics of five fruits (kiwifruit, avocado, Asian pear, persimmon, and passion fruit) was assessed by comparing the heat flux and temperature profiles of samples during the lyophilization process. For a 24 h lyophilization cycle, average heat fluxes in the primary drying phase ranged from 250 to 570 W/m2. A significant correlation was found between the temperature and heat flux distributions at the estimated endpoint of the sublimation process and the corresponding transition into the secondary drying stage. Furthermore, good agreement was also found for the freezing phase. The use of real-time heat flux measurements proved to be a cost-effective experimental method to better understand the process variables in order to reduce the lyophilization cycle time and overall energy consumption.