EUSO-SPB2 (Extreme Universe Space Observatory on a Super Pressure Balloon II) is a precursor mission for a future space observatory for multi-messenger astrophysics, planned to be launched in Spring 2023 with a flight duration target of 100 days. The Fluorescence Telescope (FT) hosted on board is designed to detect Ultra High Energy Cosmic Rays via the UV fluorescence emission of the Extensive Air Showers in the atmosphere. The Data Processor (DP) of the FT is the component of the electronics system that performs data management and instrument control for the telescope. The DP controls front-end electronics, tags events with arrival time and payload position through a GPS system, provides signals for time synchronization of the event and measures the live and dead time of the telescope. Furthermore, it manages mass memory for data storage, performs housekeeping monitoring, and controls the power-on and power-off sequences. Finally, the data processor combines the data from the PDMs and onboard differential GPS and prioritizes data for download. The long duration of the flight poses strict requirements on electronics and data handling. The operations at high altitude in an unpressurized environment represent a technological challenge for heat dissipation. This contribution will provide an overview of the innovative elements developed and the results of the integration and field test campaigns. We will also present some preliminary analysis of the performance during the flight.