<p>We present three-dimensional (3D) phase-field simulations of pressure-induced amorphization of Ge₂Sb₂​Te₅ (GST), extending our prior two-dimensional (2D) framework. The model incorporates all involving physics, i.e., elastic, thermal, and transformational strains, together with a pressure-dependent bulk modulus based on Murnaghan’s equation of state. A spherical amorphous nucleus is introduced to initiate the transformation and enable direct comparison of the amorphization pressures at onset and completion in perfect and defective materials. Results show that 3D simulations predict significantly higher amorphization pressures than the 2D scenario, with deviations up to ~ 66% at lower temperatures, underscoring the necessity of realistic geometry (2D vs. 3D) for modeling nucleation and growth. Defect studies reveal that voids reduce the amorphization threshold and accelerate transformation. Additionally, our model shows that the smaller defects and sample sizes require higher amorphization completion pressures due to limited elastic accommodation. The predicted onset and completion pressures (15–27 GPa) align well with experimental and DFT values, demonstrating the robustness of the proposed 3D model. This work highlights the critical role of dimensionality and defect morphology in pressure-induced phase transitions, providing a continuum-level pathway toward predictive modeling of chalcogenide PCMs.</p> Graphical abstract <p></p>