Characterization and extraction of plant secondary metabolites are important in agriculture, pharmaceutical, and food industry. In this regard, the applied analytical methods are mostly costly and time-consuming; therefore, choosing a suitable approach is essential for optimum results and economic suitability. One of the recently considered methods used to characterize new types of materials is MIPs. Among the various applications of MIPs is the identification and separation of various plant-derived compounds, such as secondary metabolites, chemical residues, and pesticides. The present review describes the application of MIPs as a tool in medicinal plant material analysis, focusing on plant secondary metabolism.