In this work, a comprehensive investigation of amorphous and crystalline modification of identical electrode active material as a thin-film electrode for a future all-solid-state Li-ion battery application is presented and discussed. Using the proposed micro-battery system, we aim to unravel the effect of the crystallinity of the positive electrode material on the intrinsic durability of all-solid-state thin-film Li-ion batteries during prolonged electrochemical cycling. We demonstrate the preparation, structural-, nanomechanical and electrochemical characteristics of molybdenum (VI) oxide (MoO3) thin-film cathodes based on their different crystallinity. The nanomechanical properties of the electrode layers were determined using nanoindentation along with acoustic emission studies. Based on the electrochemical test results, as-prepared thin films that did not go under any heat treatment showed the best performance and stability throughout cycling around 50 μAh initial capacity when cycled at C/2. This suits well their nanomechanical properties, which showed the highest hardness but also the highest flexibility in comparison with the heat-treated layers with lower hardness, high brittleness, and numerous cracks upon mechanical loads. According to our results, we state that amorphous-type electrode materials are more durable against electro-chemo-mechanical-aging related battery performance loss in all-solid-state Li-ion batteries compared to their crystalline counterparts.