Determining structural transformations in amorphous solids is challenging due to the paucity of structural signatures. The effect of the transitions on the properties of the solid can be significant and important for applications. Moreover, such transitions may not be discernible in the behavior of the total energy or the volume of the solid as a function of the variables that identify its phases. These issues arise in the context of lithiation of amorphous silicon (a-Si), a promising anode material for high-energy density batteries based on lithium ions. Recent experiments suggest the surprising result that the lithiation of a-Si is a two-phase process. Here, we present first-principles calculations of the structure of a-Si at different lithiation levels. Through a detailed analysis of the short and medium-range properties of the amorphous network, using Voronoi-Delaunay methods and ring statistics, we show that a-LixSi has a fundamentally different structure below and above a lithiation level corresponding to x ∼ 2.