A method of performing high throughput magnetic sensing of one or more samples. The method comprises selecting a first sample having a first bulk magnetic susceptibility, selecting an assay plate having a second bulk magnetic susceptibility matched to the first bulk magnetic susceptibility, the assay plate including multiple wells, introducing the first sample into a plurality of the wells, and performing magnetic sensing on the plurality of wells containing the first sample. Assay plates, caps, kits, and other devices and methods relating to high throughput magnetic sensing are also disclosed.