Vanadium pentaoxide, V2O5, is an attractive cathode material for Li-ion batteries, which can store up to three Li ion per formula unit. At deep discharge, an irreversible reconstructive phase transition occurs with formation of the disordered ω-LixV2O5 bronze, which, despite the lack of long-range order, exhibits a high reversible capacity (∼310 mAh/g) without regaining the crystallinity upon recharge. Here, we utilize operando powder X-ray diffraction and total scattering (i.e., pair distribution function analysis) to investigate the atomic-scale structures of the deep-discharge phase ω-LixV2O5 (x ∼ 3) and, for the first time, the highly disordered phase β-LixV2O5 (x ∼ 0.3) formed during subsequent Li-extraction. Our studies reveal that the deep discharge ω-Li3V2O5 phase consists of ∼60 Å domains rock salt structure with a local cation ordering on an ∼15 Å length scale. The charged β-LixV2O5 phase only exhibits very short-range ordering (∼10 Å). The phase transition between these phases is structurally reversible and appears unexpectedly to occur via a two-phase transition mechanism.