In situ magnetic resonance (MR) techniques, such as nuclear MR and MR imaging, have recently gained significant attention in the battery community because of their ability to provide real-time quantitative information regarding material chemistry, ion distribution, mass transport, and microstructure formation inside an operating electrochemical cell. MR techniques are non-invasive and non-destructive, and they can be applied to both liquid and solid (crystalline, disordered, or amorphous) samples. Additionally, MR equipment is available at most universities and research and development centers, making MR techniques easily accessible for scientists worldwide. In this review, we will discuss recent research results in the field of in situ MR for the characterization of Li-ion batteries with a particular focus on experimental setups, such as pulse sequence programming and cell design, for overcoming the complications associated with the heterogeneous nature of energy storage devices. A comprehensive approach combining proper hardware and software will allow researchers to collect reliable high-quality data meeting industrial standards.