The article presents a Hall effect magnetometer for use in a desktop Electron Paramagnetic Resonance spectrometer with a permanent magnet system and scanning coils. High accuracy and long-term stability at a small size and low cost are achieved through the use of digital signal processing, sequential data filtering in the time and frequency domains, as well as digital correction of raw data based on calibration information. The exciting current of the Hall sensor has the form of an alternating-sign square wave formed by a high-speed H-bridge powered by a stable direct current. Generation of control signals, time selection of data, and their accumulation are performed using Xilinx Field-Programmable Gate Array Artix-7. MicroBlaze embedded 32-bit processor is used to control the magnetometer and interface with adjacent levels of the control system. Taking into account the individual characteristics of the sensor, including the offset voltage, the nonlinearity of the magnetic sensitivity, and their temperature dependences, is carried out by correcting the data obtained by calculating a polynomial depending on the raw magnitude of the field induction and the temperature of the sensor. The polynomial coefficients are individual for each sensor, are determined once during the calibration process, and are stored in the dedicated Electrically Erasable Programmable Read-Only Memory. The magnetometer has a high resolution of 0.1 μT and an absolute measurement error of not exceeding 6 μT. © 2023 Author(s).