Solvent engineering is a powerful and versatile method to tune colloidal stability. Here, we link the molecular structure of apolar ligand shells on gold nanoparticles with their colloidal stability in solvent mixtures. The agglomeration temperature of the particles was measured with small-angle X-ray scattering. It depended on solvent composition and changed linearly for hexane–hexadecane mixtures, but nonlinearly for cyclohexane–hexadecane and hexanol–hexadecane mixtures. Molecular dynamics (MD) simulations indicate that agglomeration is dominated by temperature-dependent ligand order in the alkane mixtures and that the temperature at which the ligand shell orders depends on the solvent composition near the ligands, which can differ substantially from the bulk composition. Small-angle neutron scattering confirmed that, at intermediate solvent compositions above the agglomeration temperature, the fraction of cyclohexane near the ligands was larger than in the bulk. The enrichment of cyclohexane near the ligands stabilized their disordered state, which, consequently, led to the experimentally observed nonlinear trend of the agglomeration temperature. In contrast, hexanol was depleted from the ligand shell at all temperatures. This again stabilized the disordered state. Furthermore, we found that agglomeration at high hexanol fractions was driven by a solvophobic effect that exceeded the influence of ligand order. The results show that strong nonlinearities in the colloidal stability of nanoparticle dispersions in solvent mixtures are directly linked to the molecular details of ligand–solvent and solvent–solvent interactions, which can be used to precisely tune stability.