A quantitative assessment of Li transport is decisive for Li ion battery research. Here, we demonstrate in situ and in-operando depth profiling of the Li-inventory in lithium thin film batteries. We employ non-destructive coincidence elastic recoil detection analysis using different projectile ions in the MeV range to simultaneously quantify the lithium depth distribution in the whole stack with resolution better than 50 nm by simulations of experimental data. Experiments were performed while charging and discharging the stack. 5 MeV 7Li primary ions were employed to extract the Li depth distribution in an ∼3.6 μm thick Ti/LMO/LIPON/NbO/Ti thin film battery. To show the versatility of the approach, a coincidence experiment was also performed using 4 MeV He ions for an ∼3.4 μm thick Ti/LMO/LIPON/NbO/Ti battery. Our results illustrate, for example, lithium accumulation in the 90 nm thick NbO layer upon charging with +3 V. We could also show the transport of large amounts of Li from the LMO/LIPON interface to the LIPON/NbO interface upon overcharging with +5 V. Altogether, these experiments demonstrate the potential of the employed technique, enabling in-operando high resolution composition depth profiling of Li and other light elements (e.g., H, He, C, N, and O) in ultrathin all-solid state batteries.