The design of molecular magnets using the "porosity" concept seen in metal-organic frameworks (MOFs) is a unique direction for potential applications such as magnetic sensors, switches, and nonvolatile electromagnets. In addition, the strategy of "magnet + porosity" could allow for the creation of postsynthesized magnets often exhibiting a higher magnetic phase transition temperature (Tc) than a self-assembled magnet. A class of paramagnetic MOFs with electron-acceptor ligands, which can accept electrons from an appropriate donor or electrode to form organic radicals, shows great promise, because their magnetic phase stability is tuned through an external electron-filling control. Here, we demonstrate the electrochemical switching of nonvolatile magnetic phases in the well-known honeycomb-layer ferrimagnet (NBu4)[MnIICrIII(Cl2An)3] (H2Cl2An = 2,5-dichloro-3,6-dihydroxy-1,4-benzoquinone) using a Li ion battery (LIB) system, in which Li+ ions and electrons are simultaneously inserted into or extracted from the material. Ferrimagnetic phase stability is reversibly modulated using in situ LIB discharge/charge cycles.