Trace concentrations of iron oxide minerals in carbonate sediments can preserve fine details about Earth processes, from high-resolution recordings of the Earth's ancient magnetic field to microscopic remnants of extraterrestrial impacts. This paper presents a novel flask extraction method which uses a neodymium magnet and an orbital shaker for simple and efficient separation of magnetic minerals from carbonate sediments. A mineral assemblage of magnetic standards (titanomagnetite, magnetite, goethite, and hematite) combined with other mineral standards (kaolinite, quartz, and nanoscale TiO2) was subjected to the extraction procedure and compared to a natural speleothem sample. Exposure of the magnetic standards to a mildly acidic acetate buffer (pH ∼ 4) did not cause physical or chemical alteration. The strongly magnetic minerals were reproducibly extracted, with greater than 90% efficiency (by mass), from mixtures of the mineral standards. XRD and low-temperature magnetic characterization demonstrated phase purity of the extracts. Quantitative comparison with two commonly used literature methods showed that the flask extraction method was more reproducible and efficient. The addition of surfactant (Na(PO3)6) did not significantly improve extraction efficiency. Sequential dissolution and flask extraction of a simulated speleothem containing magnetic particles resulted in consistent extraction efficiencies for samples containing large (> 1 µm) strongly magnetic grains, but a reduction in efficiency was observed for smaller (< 1 µm) grain sizes. No method successfully extracted the weakly magnetic goethite and hematite. However, unprecedented, representative characterization of these minerals was possible through quantitative analysis of the remainder after the collection of the magnetic extract. This approach may facilitate detailed characterization of a wide range of carbonates, such as pelagic limestone, dolostone, unlithified carbonate ooze, speleothems, and freshwater and pedogenic carbonates. Such mineral extractions can lead to new insights into paleoenvironmental processes as well as an improved understanding of the recording of the Earth's magnetic field.