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Abstract Segregation to grain boundaries affects their cohesion, corrosion, and embrittlement and plays a critical role in heterogeneous nucleation. In order to quantitatively study segregation and low-dimensional phase separation at grain boundaries, here, we apply a density-based phase-field model. The current model describes the grain-boundary thermodynamic properties based on available bulk thermodynamic data, while the grain-boundary-density profile is obtained using atomistic simulations. To benchmark the performance of the model, Mn grain-boundary segregation in the Fe–Mn system is studied. 3D simulation results are compared against atom probe tomography measurements conducted for three alloy compositions. We show that a continuous increase in the alloy composition results in a discontinuous jump in the segregation isotherm. The jump corresponds to a spinodal phase separation at grain boundary. For alloy compositions above the jump, we reveal an interfacial transient spinodal phase separation. The transient spinodal phenomenon opens opportunities for knowledge-based microstructure design through the chemical manipulation of grain boundaries. The proposed density-based model provides a powerful tool to study thermodynamics and kinetics of segregation and phase changes at grain boundaries.