X-ray microscopy is powerful in that it can probe large volumes of material at high spatial resolution with exquisite chemical, electronic and bond orientation contrast. The development of diffraction-based methods such as ptychography has, in principle, removed the resolution limit imposed by the characteristics of the X-ray optics. Here, using soft X-ray ptychography, we demonstrate the highest-resolution X-ray microscopy ever achieved by imaging 5 nm structures. We quantify the performance of our microscope and apply the method to the study of delithiation in a nanoplate of LiFePO4, a material of broad interest in electrochemical energy storage. We calculate chemical component distributions using the full complex refractive index and demonstrate enhanced contrast, which elucidates a strong correlation between structural defects and chemical phase propagation. The ability to visualize the coupling of the kinetics of a phase transformation with the mechanical consequences is critical to designing materials with ultimate durability.