Many carbon allotropes can act as host materials for reversible lithium uptake1,2, thereby laying the foundations for existing and future electrochemical energy storage. However, insight into how lithium is arranged within these hosts is difficult to obtain from a working system. For example, the use of in situ transmission electron microscopy3–5 to probe light elements (especially lithium)6,7 is severely hampered by their low scattering cross-section for impinging electrons and their susceptibility to knock-on damage8. Here we study the reversible intercalation of lithium into bilayer graphene by in situ low-voltage transmission electron microscopy, using both spherical and chromatic aberration correction9 to enhance contrast and resolution to the required levels. The microscopy is supported by electron energy-loss spectroscopy and density functional theory calculations. On their remote insertion from an electrochemical cell covering one end of the long but narrow bilayer, we observe lithium atoms to assume multi-layered close-packed order between the two carbon sheets. The lithium storage capacity associated with this superdense phase far exceeds that expected from formation of LiC6, which is the densest configuration known under normal conditions for lithium intercalation within bulk graphitic carbon10. Our findings thus point to the possible existence of distinct storage arrangements of ions in two-dimensional layered materials as compared to their bulk parent compounds.