PurposeQuantitative susceptibility mapping (QSM) estimates the spatial distribution of tissue magnetic susceptibilities from the phase of a gradient‐echo signal. QSM algorithms require a signal mask to delineate regions with reliable phase for subsequent susceptibility estimation. Existing masking techniques used in QSM have limitations that introduce artifacts, exclude anatomical detail, and rely on parameter tuning and anatomical priors that narrow their application. Here, a robust masking and reconstruction procedure is presented to overcome these limitations and enable automated QSM processing. Moreover, this method is integrated within an open‐source software framework: QSMxT.MethodsA robust masking technique that automatically separates reliable from less reliable phase regions was developed and combined with a two‐pass reconstruction procedure that operates on the separated sources before combination, extracting more information and suppressing streaking artifacts.ResultsCompared with standard masking and reconstruction procedures, the two‐pass inversion reduces streaking artifacts caused by unreliable phase and high dynamic ranges of susceptibility sources. It is also robust across a range of acquisitions at 3 T in volunteers and phantoms, at 7 T in tumor patients, and in an in silico head phantom, with significant artifact and error reductions, greater anatomical detail, and minimal parameter tuning.ConclusionThe two‐pass masking and reconstruction procedure separates reliable from less reliable phase regions, enabling a more accurate QSM reconstruction that mitigates artifacts, operates without anatomical priors, and requires minimal parameter tuning. The technique and its integration within QSMxT makes QSM processing more accessible and robust to streaking artifacts.