This paper describes an acoustic phonon-based characterization technique as a novel tool for the characterization of dynamic microelectromechanical (MEMS) devices such as resonators, switches, micromirrors, accelerometers and gyroscopes. The technique intrinsically features non-invasive characterization due to the favorable transmission properties of acoustic phonons through device packaging and high throughput due to universal detectability from a single detection point, which facilitates high volume wafer and package level testing. The dependence of phonon generation on material properties yields information not obtained in existing electrical, optical and electron beam testing techniques such as contact tribology, energy dissipation, non-linear device behavior and device resonance modes. Preliminary case study results show that phonon-based characterization not only provides efficient, non-destructive testing (NDT) of MEMS functionality, but also insights into MEMS device lifecycle behavior.