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The ever-increasing demand for high-capacity rechargeable batteries highlights the need for sensitive and accurate diagnostic technology for determining the state of a cell, for identifying and localizing defects, and for sensing capacity loss mechanisms. Here, we leverage atomic magnetometry to map the weak induced magnetic fields around Li-ion battery cells in a magnetically shielded environment. The ability to rapidly measure cells nondestructively allows testing even commercial cells in their actual operating conditions, as a function of state of charge. These measurements provide maps of the magnetic susceptibility of the cell, which follow trends characteristic for the battery materials under study upon discharge. In particular, hot spots of charge storage are identified. In addition, the measurements reveal the capability to measure transient internal current effects, at a level of μA, which are shown to be dependent upon the state of charge. These effects highlight noncontact battery characterization opportunities. The diagnostic power of this technique could be used for the assessment of cells in research, quality control, or during operation, and could help uncover details of charge storage and failure processes in cells.