We used in situ neutron powder diffraction (NPD) to study the migration of Li in Li4Ti5O12 anodes with different particle sizes during battery cycling. The motivation of this work was to uncover the mechanism of the increased capacity of the battery made with a smaller-particle-sized anode. In real time, we monitored the anode lattice parameter, Li distribution, and oxidation state of the Ti atom, and these suggested an increase in the rate of Li incorporation into the anode rather than a change in the migration pathway as a result of the particle size reduction. The lattice of these anodes during continuous lithiation undergoes expansion followed by a gradual contraction and then expansion again. The measured lattice parameter changes were reconciled with Li occupation at specific sites within the Li4Ti5O12 crystal structure, where Li migrates from the 8a to 16c sites. Despite these similar Li-diffusion pathways, in larger-particle-sized Li4Ti5O12 the population of Li at the 16c site is accompanied by Li depopulation from the 8a site, which is in contrast to the smaller-particle-sized anode where our results suggest that Li at the 8a site is replenished faster than the rate of transfer of Li to the 16c site. Fourier-difference nuclear density maps of both anodes suggest that 32e sites are involved in the diffusion pathway of Li. NPD is again shown to be an excellent tool for the study of electrode materials for Li-ion batteries, particularly when it is used to probe real-time crystallographic changes of the materials in an operating battery during charge–discharge cycling.