Control of the homogenization process is important in obtaining high extrudability and desirable properties in 6xxx aluminum alloys. Three consecutive steps of the process chain were modeled. Microsegregation arising from solidification was described with the Scheil–Gulliver model. Dissolution of Mg2Si, Si (diamond) and β-AlFeSi (β-Al5FeSi) to α-AlFeSi (α-Al12(FeMn)3Si) transformation during homogenization have been described with a CALPHAD-based multicomponent diffusion Dual-Grain Model (DGM), accounting for grain size inhomogeneity. Mg2Si precipitation and associated strengthening during homogenization cooling were modeled with the Kampmann–Wagner Numerical (KWN) precipitation framework. The DGM model indicated that the fractions of β-AlFeSi and α-AlFeSi exhibit an exact spatial and temporal correspondence during transformation. The predictions are in good agreement with experimental data. The KWN model indicated the development of a bimodal particle size distribution during homogenization cooling, arising from corresponding nucleation events. The associated strengthening, arising from solid solution and precipitation strengthening, was in good agreement with experimental results. The proposed modeling approach is a valuable tool for the prediction of microstructure evolution during the homogenization of 6xxx aluminum alloys, including the often-neglected part of homogenization cooling.