As the complexity of mechanically interlocked molecular architectures increases, it is important to understand the underlying principles, such as molecular recognition and self-assembly processes, that govern the practice of template-directed synthesis necessary to create these particular compounds. In this review, we explain the importance of dynamic processes in the synthesis of mechanically interlocked compounds. We show how many different dynamic covalent bonds have been used in the synthesis of rotaxanes, catenanes, and other higher-order mechanically interlocked compounds, with the goal of revealing the state of the art in dynamic covalent chemistry.