The LHCb experiment, one of the four operating in the LHC, will be enduring a major upgrade of its electronics during the third long shutdown period of the particle accelerator. One of the main objectives of the upgrade effort is to implement a 40MHz readout of collision data. For this purpose, the Front-End electronics will make extensive use of a radiation resistant chipset, the Gigabit Transceiver (GBT), for readout as well as for slow control, monitoring and synchronization. At LHCb, the tools to operate the front-end electronics are developed by a central team and distributed to the users. This contribution describes the architecture of the system that implements the slow control and monitoring of all Front-End electronics using the GBT chipset, namely the GBTx and GBT-SCA. The system is implemented in 3 layers starting with an FPGA based electronic board that interfaces the GBT chipset directly through optical fibers. The second layer is composed by a PCIe driver and a number of processes to operate these boards. The user operates the system in the third layer which is the WinCC OA SCADA that is interfaced with the Front-Ends via a message broker called DIM. The requirements of the system as well as the design and integration of each layer are discussed in detail. The results of the firmware implementation in hardware and operational tests are shown and the overall performance of the system is discussed.