Lithium ion batteries are a leading energy storage technology for electronic portable devices and hybrid electric vehicles. A long-standing challenge to understand Li ion transport is the fact that this light atom escapes direct detection by X-ray techniques (EDX, XRD and XAS) due to weak scattering and emission properties. Simultaneous characterisation of the structure, chemical composition (including Li) and elemental distribution in Li-ion battery materials can reveal the relationship between Li ion transport and structural effects (phase transformation, internal stress), and battery performance and degradation. Nanoscale mapping is achieved by multi-modal correlative microscopy combining focused ion beam and scanning electron microscopy (FIB-SEM) with Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS). Mapping Li, Mn and Co nanoscale distributions reveals the micro-structural consequences of the electrochemical reaction, and allows identifying Li “trapping” sites within the structure that control materials properties, and open the way towards designing better Li-ion cathode materials with superior performance.