Tuning magnetic properties in layered van der Waals (vdW) materials has captured significant attention due to the efficient control of ground states by heterostructuring and external stimuli. Electron doping by electrostatic gating, interfacial charge transfer, and intercalation is particularly effective in manipulating the exchange and spin-orbit properties, resulting in a control of Curie temperature (TC) and magnetic anisotropy. Here, an uncharted role of intercalation is discovered to generate magnetic frustration. As a model study, Na atoms are intercalated into the vdW gaps of pristine Cr2Ge2Te6 (CGT) where generated magnetic frustration leads to emerging spin-glass states coexisting with a ferromagnetic order. A series of dynamic magnetic susceptibility measurements/analysis confirms the formation of magnetic clusters representing slow dynamics with a distribution of relaxation times. The intercalation also modifies other macroscopic physical parameters including the significant enhancement of TC from 66 to 240K and the switching of magnetic easy-hard axis direction. This study identifies intercalation as a unique route to generate emerging frustrated spin states in simple vdW crystals.