We study the dynamics of a qubit coupled to an acoustic resonator by a piezoelectric film. By varying the surface topography of the resonator from rough to polished to shaped, we explore the crossover from fast decay of an excited qubit to quantum-coherent coupling between the qubit and an isolated phonon mode. Our experimental approach may be used for precision measurements of crystalline vibrations, the design of quantum memories, and the study of electro-mechanical contributions to dielectric loss.