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Abstract Interest in magnetic fields on the ancient Earth and other planetary bodies has motivated the paleomagnetic analysis of complex rocks such as meteorites that carry heterogeneous magnetizations at <<1 mm scales. The net magnetic moment of natural remanent magnetization (NRM) in such small samples is often below the detection threshold of common cryogenic magnetometers. The quantum diamond microscope (QDM) is an emerging magnetic imaging technology with ~1 μm resolution and can, in principle, recover magnetizations as weak as 10⁻¹⁷ Am². However, the typically 1–100 μm sample‐to‐sensor distance of QDM measurements can result in complex (nondipolar) magnetic field maps, from which the net magnetic moment cannot be determined using a simple algorithm. Here we generate synthetic magnetic field maps to quantify the errors introduced by sample nondipolarity and by map processing procedures such as upward continuation. We find that inversions based on least squares dipole fits of upward continued data can recover the net moment of complex samples with <5% to 10% error for maps with signal‐to‐noise ratio (SNR) in the range typical of current generation QDMs. We validate these error estimates experimentally using comparisons between QDM maps and between QDM and SQUID microscope data, concluding that, within the limitations described here, the QDM is a robust technique for recovering the net magnetic moment of weakly magnetized samples. More sophisticated net moment fitting algorithms in the future can be combined with upward continuation methods described here to improve accuracy.