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The layered crystal structure of Cr2Ge2Te6 shows ferromagnetic ordering at the two‐dimensional limit, which holds promise for spintronic applications. However, external voltage pulses can trigger amorphization of the material in nanoscale electronic devices, and it is unclear whether the loss of structural ordering leads to a change in magnetic properties. Here, it is demonstrated that Cr2Ge2Te6 preserves the spin‐polarized nature in the amorphous phase, but undergoes a magnetic transition to a spin glass state below 20 K. Quantum‐mechanical computations reveal the microscopic origin of this transition in spin configuration: it is due to strong distortions of the CrTeCr bonds, connecting chromium‐centered octahedra, and to the overall increase in disorder upon amorphization. The tunable magnetic properties of Cr2Ge2Te6 can be exploited for multifunctional, magnetic phase‐change devices that switch between crystalline and amorphous states. [ABSTRACT FROM AUTHOR]