Development in instrumentation and technology now allows for mapping of magnetic anomalies, caused by spatial variations in magnetization in the source material, from the mineral to the crustal anomalies scale. High‐resolution magnetic mapping techniques allow for accurate investigation of the magnetization in natural rock samples and particularly of their remanence carriers, which can record geologically meaningful information. Multidomain magnetic grains are expected to retain a remanence that is susceptible to change by exposure to magnetic fields or by changes in temperature. Although this makes multidomain grains less reliable remanence carriers for paleomagnetic studies, their magnetization contributes to rocks bulk magnetization and to induced anomalies in the Earth crust. Here, we investigate the fine‐scale magnetization of a sample that exhibits a multidomain behavior. We used a scanning magnetic microscope, equipped with a room temperature magnetic tunnel junction sensor, to map the magnetic field over a petrographic thin section of the sample containing large magnetite grains (>100 μm) surrounded by serpentine and carbonate. We modeled the fine‐scale remanent magnetization of the magnetite by inverting the magnetic scans data acquired in near‐field‐free conditions. We applied a multistep inversion, a priori tested on a synthetic model, with a controlled range on the intensity of the magnetization. Modeling results on the study sample suggest homogenously magnetized regions within the magnetite grains with variable remanent magnetization intensities and directions coherent with the multidomain behavior inferred from bulk measurements.