Understanding (de)lithiation heterogeneities in battery materials is key to ensuring optimal electrochemical performance and developing better energy storage devices. However, this remains challenging due to the complex three dimensional morphology of microscopic electrode particles, the involvement of both solid and liquid phase reactants, and range of relevant timescales (seconds to hours). Here, we overcome this problem and demonstrate the use of bench-top laser scanning confocal microscopy for simultaneous three-dimensional operando measurement of lithium ion dynamics in single particles, and the electrolyte, in batteries. We examine two technologically important cathode materials that are known to suffer from intercalation heterogeneities: LixCoO2 and LixNi0.8Mn0.1Co0.1O2. The single-particle surface-to-core transport velocity of Li-phase fronts, and volume changes – as well as their inter-particle heterogeneity – are captured as a function of C-rate, and benchmarked to previous ensemble measurements. Additionally, we visualise heterogeneities in the bulk and at the surface of particles during cycling, and image the formation of spatially non-uniform concentration gradients within the liquid electrolyte. Importantly, the conditions under which optical imaging can be performed inside absorbing and multiply scattering materials such as battery intercalation compounds are outlined.