Abstract: Systems and methods are disclosed for automatically calibrating a magnetometer during user activity. A portable device associated with a user provides magnetic field measurements during user activity, which are converted to a frequency domain and frequency component(s) that correspond to the user activity are distinguished. A criterion is defined for the distinguished frequency components such that magnetometer bias is estimated by satisfying a condition for the criterion. Accordingly, the estimated magnetometer bias may be applied to the obtained magnetic field measurements. The calibrated magnetic field measurements may be used for any suitable purposes, including for building a magnetic fingerprint map using crowdsourcing techniques.