Sampling on different substrates is commonly used in laboratory and field studies to investigate the morphology and mixing state of aerosol particles. Our focus was on the transformations that can occur to the collected particles during storage, handling, and analysis. Particle samples were prepared by electrostatic deposition of size-classified sodium chloride, sulfuric acid, and coated soot aerosols on different substrates. The samples were inspected by electron microscopy before and after exposure to various environments. For coated soot, the imaging results were compared against mass-mobility measurements of airborne particles that underwent similar treatments. The extent of sample alteration ranged from negligible to major, depending on the environment, substrate, and particle composition. We discussed the implications of our findings for cases where morphology and the mixing state of particles must be preserved, and cases where particle transformations are desirable.