Attaching field-programmable gate arrays to microcontrollers deployed in the field can increase their potential applications. Making these systems reconfigurable post-deployment effectively makes them future-proof, allowing maintenance and updating of firmware in distributed computing applications. This paper presents UpGate, an embedded software that can securely perform an over-the-air update of an FPGA’s function with minimal communication overhead, enabling complete flexibility of the device’s functionality. Several benchmarks are performed using simple to complex hardware designs for in-depth analysis of memory footprint, timings, and power consumption. The results show that regular lossless compression techniques, such as GZip and LZ4, with 80% compression rate in the worst case, are reducing the global binary update duration by at least 4 times. This represents 15 times less 128 B packets transmitted, and approximately 40 s to transfer a RISC-V core bitstream of 579 kB. Surprisingly, what takes the most time and energy is writing to flash.