This Letter proposes a design strategy leveraging tunable structural defects in multi-stable mechanical metamaterials for manipulating the propagation of the supported transition waves toward the endowment of a multi-phase patterning capability. The defect reversibly adjusts the on-site potential in order to affect the motion of the transition waves which traverse it, either prohibiting wave transmission (i.e., stabilization) or permitting transmission of specific modes, possibly converting one mode into another. Thus, the defect is able to control the occurrence and distribution of the structural phases and realize the desired phase patterns. Although the metamaterial model for our analytical and numerical study is a one-dimensional (1D) architecture comprising tri-stable elements, the proposed method is shown to apply to 2D architectures and is amenable to elements possessing more than three stable states, demonstrating greater flexibility in metamaterial design than current approaches. The proposed method expands the configuration space of phase-transforming metamaterials, which contributes to efforts aimed at re-programmable mechanical/dynamic performance.