The authors report on the structural and optical property changes of alumina passivated amorphous Si slanted columnar thin films during electrochemical Li-ion intercalation and deintercalation determined by in situ generalized spectroscopic ellipsometry. The cyclic voltammetry investigations versus Li/Li+ are performed at a rate of 1mV/s, while Mueller matrix generalized spectroscopic ellipsometry data are collected. Through a best-match model analysis utilizing the homogeneous biaxial layer approach, temporal anisotropic optical constants are obtained. The authors observe a strong anisotropic electrochromic response with maximum changes of similar to 18% in the anisotropic refractive indices and similar to 750% in the anisotropic extinction coefficients. Furthermore, the thin films reversibly expand and contract by similar to 35%. A comparative analysis of the temporal optical constant response to the changes in overall optical anisotropy of the electrode reveals six transient regions throughout the Li-ion intercalation and deintercalation cycle of the highly ordered three-dimensional nanostructures. The transients correspond to electrochemical potential regions which show limited charge transfer, metalization or demetalization, and swelling or deswelling of the nanostructures. Furthermore, the electrochemical potential regions in which the transients are observed here are very similar to those previously reported for Li-ion intercalation and deintercalation of silicon nanowires using structural analysis techniques, where four distinct phases of Li-Si alloy formation were revealed. The authors find that at low Li contributions, swelling and deswelling occur preferentially along the slanted columns, while at high Li contributions, swelling and deswelling occur preferentially within the intercolumnar space. (C) 2017 American Vacuum Society.