The formation of metallic lithium microstructures in the form of dendrites or mosses at the surface of anode electrodes (e.g., lithium metal, graphite, and silicon) leads to rapid capacity fade and poses grave safety risks in rechargeable lithium batteries. We present here a direct, relative quantitative analysis of lithium deposition on graphite anodes in pouch cells under normal operating conditions, paired with a model cathode material, the layered nickel-rich oxide LiNi0.61Co0.12Mn0.27O2, over the course of 3000 charge-discharge cycles. Secondary-ion mass spectrometry chemically dissects the solid-electrolyte interphase (SEI) on extensively cycled graphite with virtually atomic depth resolution and reveals substantial growth of Li-metal deposits. With the absence of apparent kinetic (e.g., fast charging) or stoichiometric restraints (e.g., overcharge) during cycling, we show lithium deposition on graphite is triggered by certain transition-metal ions (manganese in particular) dissolved from the cathode in a disrupted SEI. This insidious effect is found to initiate at a very early stage of cell operation (<200 cycles) and can be effectively inhibited by substituting a small amount of aluminum (∼1 mol %) in the cathode, resulting in much reduced transition-metal dissolution and drastically improved cyclability. Our results may also be applicable to studying the unstable electrodeposition of lithium on other substrates, including Li metal.