Mineral magnetism of Pau d'Alho cave sediments, soils outside the cave, and in the stalagmite #6 (ALHO6) in Midwest Brazil is presented. This high growth‐rate speleothem (~168 mm/ka) encompasses the past 1355 years. Oxygen and carbon isotope data from the same stalagmite allow for a direct comparison of the magnetic signal with changes in paleoprecipitation and soil dynamics at the surface. Magnetic experiments include isothermal remanent magnetization, anhysteretic remanent magnetization, hysteresis loops, first‐order reversal curves, and low‐temperature superconducting quantum interference device magnetometry. The main magnetic remanence carriers in ALHO6 are magnetite and goethite, with a nearly constant relative proportion. Remanent coercivities of magnetite in all our samples are within 14–17 mT for an average grain‐size of ~1–2 µm, in the range of pedogenic magnetite, thus suggesting the detrital grains deposited in the stalagmite were produced in the soil above the cave. Magnetic remanence variations follow δ13C and δ18O data, suggesting a climatic control on the input of magnetic minerals into the Pau d'Alho cave system. The concentration of magnetic minerals in the stalagmite is governed by soil erosion above the cave, which by its turn is controlled by soil erosion and vegetation cover. Dry periods are associated with less stable soils and result in higher mineral fluxes carried into karst systems. Conversely, wetter periods are associated with soils topped by denser vegetation that retains micrometer‐scale pedogenic minerals and thus reduces detrital fluxes into the cave.