A magnetometer system comprising: a sensor cell (12, 50) comprising alkali metal particles and at least one nuclear spin isotope; a probe laser configured to provide a probe beam (O PRB) through the sensor cell (12, 50) to generate a detection beam (O DET); a magnetic field system configured to generate a plurality of magnetic fields (Bx, B Y, B Z) through a respective plurality of axes (54, 56, 58) through the sensor cell (12, 50); a detection system configured to implement detection of an external magnetic field based on characteristics of the detection beam (O DET) in response to precession of the alkali metal particles and the at least one nuclear spin isotope based on the plurality of magnetic fields (B X, B Y, B Z); and a calibration controller comprising: a current controller configured to control a plurality of currents that are associated with the respective plurality of magnetic fields (B X, B Y, B Z), the current controller being configured to square-wave modulate at least one of the plurality of currents about a DC baseline amplitude; and a frequency monitor configured to monitor the precession frequency of the at least one nuclear spin isotope at each modulated amplitude of the at least one of the plurality of currents (Ix, I Y, Iz), the current controller being further configured to adjust the DC baseline amplitude in a feedback manner to set the precession frequency of the at least one nuclear spin isotope equal with respect to square-wave modulation amplitudes of each of the at least one of the plurality of currents (Ix, I Y, Iz) to determine the DC baseline amplitude corresponding to a zero net magnetic field amplitude along a respective one of three orthogonal axes corresponding to the respective one of the at least one of the plurality of currents (Ix, I Y, Iz) as determined by the frequency monitor to calibrate the magnetometer system. a sensor cell (12, 50) comprising alkali metal particles and at least one nuclear spin isotope; a probe laser configured to provide a probe beam (O PRB) through the sensor cell (12, 50) to generate a detection beam (O DET); a magnetic field system configured to generate a plurality of magnetic fields (Bx, B Y, B Z) through a respective plurality of axes (54, 56, 58) through the sensor cell (12, 50); a detection system configured to implement detection of an external magnetic field based on characteristics of the detection beam (O DET) in response to precession of the alkali metal particles and the at least one nuclear spin isotope based on the plurality of magnetic fields (B X, B Y, B Z); and a calibration controller comprising: a current controller configured to control a plurality of currents that are associated with the respective plurality of magnetic fields (B X, B Y, B Z), the current controller being configured to square-wave modulate at least one of the plurality of currents about a DC baseline amplitude; and a frequency monitor configured to monitor the precession frequency of the at least one nuclear spin isotope at each modulated amplitude of the at least one of the plurality of currents (Ix, I Y, Iz), the current controller being further configured to adjust the DC baseline amplitude in a feedback manner to set the precession frequency of the at least one nuclear spin isotope equal with respect to square-wave modulation amplitudes of each of the at least one of the plurality of currents (Ix, I Y, Iz) to determine the DC baseline amplitude corresponding to a zero net magnetic field amplitude along a respective one of three orthogonal axes corresponding to the respective one of the at least one of the plurality of currents (Ix, I Y, Iz) as determined by the frequency monitor to calibrate the magnetometer system. a current controller configured to control a plurality of currents that are associated with the respective plurality of magnetic fields (B X, B Y, B Z), the current controller being configured to square-wave modulate at least one of the plurality of currents about a DC baseline amplitude; and a frequency monitor configured to monitor the precession frequency of the at least one nuclear spin isotope at each modulated amplitude of the at least one of the plurality of currents (Ix, I Y, Iz), the current controller being further configured to adjust the DC baseline amplitude in a feedback manner to set the precession frequency of the at least one nuclear spin isotope equal with respect to square-wave modulation amplitudes of each of the at least one of the plurality of currents (Ix, I Y, Iz) to determine the DC baseline amplitude corresponding to a zero net magnetic field amplitude along a respective one of three orthogonal axes corresponding to the respective one of the at least one of the plurality of currents (Ix, I Y, Iz) as determined by the frequency monitor to calibrate the magnetometer system.