AbstractThe magnetic properties of van der Waals materials are profoundly influenced by structural defects. The layered antiferromagnet MnPS3 offers a unique opportunity to explore defect‐related magnetism, as Mn2+ vacancies can be generated by the intercalation of specific guest molecules. However, the effectiveness of this process in atomically thin flakes and the extent of the magnetic tunability remain unclear. Here, it is shown that the magnetic properties of MnPS3 can be tailored through the intercalation of different guest molecules. Notably, the insertion of four alkylammonium ions introduces different populations of Mn2+ vacancies, leading to a transition from the pristine antiferromagnetic state to more complex magnetic textures, including a ferrimagnetic state displaying a magnetic saturation of 1 µB per atom. Moreover, it is shown that the intercalation of few‐nm‐thick flakes also leads to the emergence of a ferrimagnetic response. This in‐flake intercalation, which can be monitored in real time using optical microscopy, can be interrupted before completion, generating lateral heterostructures between pristine and intercalated areas. This approach opens the way to the use of partial intercalation to define regions with distinct magnetic properties within a single flake.