We improved a magnetic scanning microscope for measuring the magnetic properties of minerals in thin sections of geological samples at submillimeter scales. The microscope is comprised of a 200 µm diameter Hall sensor that is located at a distance of 142 µm from the sample; an electromagnet capable of applying up to 500 mT DC magnetic fields to the sample over a 40 mm diameter region; a second Hall sensor arranged in a gradiometric configuration to cancel the background signal applied by the electromagnet and reduce the overall noise in the system; a custom-designed electronics system to bias the sensors and allow adjustments to the background signal cancelation; and a scanning XY stage with micrometer resolution. Our system achieves a spatial resolution of 200 µm with a noise at 6.0 Hz of 300 nT rms /(Hz) 1/2 in an unshielded environment. The magnetic moment sensitivity is 1.3 × 10 −11 Am 2 . We successfully measured the representative magnetization of a geological sample using an alternative model that takes the sample geometry into account and identified different micrometric characteristics in the sample slice.