Mechanochemical synthesis is a powerful approach to obtain new materials, limiting costs, and times. However, defected and submicrometrical-sized crystal products make critical their characterization through classical single-crystal X-ray diffraction. A valid alternative is represented by three-dimensional (3D) electron diffraction, in which a transmission electron microscope is used, like a diffractometer. This work matches a green waterbased mechanochemical synthesis and 3D electron diffraction to obtain and characterize a Cu-based protocatechuate metal−organic framework (PC-MOF). Its structure has been fully refined through dynamical diffraction theory, and free water molecules could be detected in the channels of the framework. Thermal characterization, focused on the dehydration profile determination, leads to the formation of a novel high-temperature 2D coordination polymer, fully solved with 3D electron diffraction data. At last, the strong activity of the PC-MOF against cationic dyes like methylene blue has been reported.