Evidence has accumulated that secondary organic aerosols (SOAs) exhibit complex morphologies with multiple phases that can adopt amorphous semisolid or glassy phase states. However, experimental analysis and numerical modeling on the formation and evolution of SOA still often employ equilibrium partitioning with an ideal mixing assumption in the particle phase. Here we apply the kinetic multilayer model of gas–particle partitioning (KM-GAP) to simulate condensation of semi-volatile species into a core–shell phase-separated particle to evaluate equilibration timescales of SOA partitioning. By varying bulk diffusivity and the activity coefficient of the condensing species in the shell, we probe the complex interplay of mass transfer kinetics and the thermodynamics of partitioning. We found that the interplay of non-ideality and phase state can impact SOA partitioning kinetics significantly. The effect of non-ideality on SOA partitioning is slight for liquid particles but becomes prominent in semisolid or solid particles. If the condensing species is miscible with a low activity coefficient in the viscous shell phase, the particle can reach equilibrium with the gas phase long before the dissolution of concentration gradients in the particle bulk. For the condensation of immiscible species with a high activity coefficient in the semisolid shell, the mass concentration in the shell may become higher or overshoot its equilibrium concentration due to slow bulk diffusion through the viscous shell for excess mass to be transferred to the core phase. Equilibration timescales are shorter for the condensation of lower-volatility species into semisolid shell; as the volatility increases, re-evaporation becomes significant as desorption is faster for volatile species than bulk diffusion in a semisolid matrix, leading to an increase in equilibration timescale. We also show that the equilibration timescale is longer in an open system relative to a closed system especially for partitioning of miscible species; hence, caution should be exercised when interpreting and extrapolating closed-system chamber experimental results to atmosphere conditions. Our results provide a possible explanation for discrepancies between experimental observations of fast particle–particle mixing and predictions of long mixing timescales in viscous particles and provide useful insights into description and treatment of SOA in aerosol models.