Silicon-containing Li-ion batteries have been the focus of many energy storage research efforts because of the promise of high energy density. Depending on the system, silicon generally demonstrates stable performance in half-cells, which is often attributed to the unlimited lithium supply from the lithium (Li) metal counter electrode. Here, the electrochemical performance of silicon with a high voltage NMC622 cathode was investigated in superconcentrated phosphonium-based ionic liquid (IL) electrolytes. As a matter of fact, there is very limited work and understanding of the full cell cycling of silicon in such a new class of electrolytes. The electrochemical behavior of silicon in the various IL electrolytes shows a gradual and steeper capacity decay, compared to what we previously reported in half-cells. This behavior is linked to a different evolution of the silicon morphology upon cycling, and the characterization of cycled electrodes points toward mechanical reasons, complete disconnection of part of the electrode, or internal mechanical stress, due to silicon and Li metal volume variation upon cycling, to explain the progressive capacity fading in full cell configuration. An extremely stable solid electrolyte interphase (SEI) in the full Li-ion cells can be seen from a combination of qualitative and quantitative information from transmission electron microscopy, X-ray photoelectron spectroscopy, electrochemical impedance spectroscopy, and magic angle spinning nuclear magnetic resonance. Our findings provide a new perspective to full cell interpretation regarding capacity fading, which is oftentimes linked almost exclusively to the loss of Li inventory but also more broadly, and provide new insights into the impact of the evolution of silicon morphology on the electrochemical behavior.