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Electromagnetic Interference and Compatibility (EMI–EMC) are a serious problem in Microelectromechanical Systems (MEMS), and specially in powered by wireless energy transfer MEMS. Most MEMS have dimensions in the order of 1 mm or less, thus, most of the suitable electromagnetic radiation sources have wavelengths larger than this, making isolation of electromagnetic effects very difficult. Model‐Based Systems Engineering (MBSE) can be an excellent tool to deal with EMI—EMC in MEMS during early design phases. In this work, we present a problem‐solving procedure and integration of EMI—EMC in MEMS from a Model‐Based Systems Engineering perspective. This approach is described in detail by a real example using a procedure based on nine steps fully integrated with the proposed systems engineering methodology. For example, the use of context diagrams (IBDs) and N SQUARE charts to describe EMC interactions is explained in detail. The system is formed by a Wireless Power Transfer (WPT) subsystem working near 2.45 or 4.5 GHz coupled to an electromagnetic micromotor. This micromotor contains copper microcoils which can receive electromagnetic radiation directly at the same time that the WPT subsystem. The greatest difficulty is, then, to power the WPT while isolating the micromotor, and optimizing the coupling interface. A summary of the most important EMC concepts and tools are reviewed from the systems engineer perspective and possible problems during the design and testing phases are discussed in detail using the example. [ABSTRACT FROM AUTHOR]