CsPbBr₃ nanocrystals (NCs) suffer from instabilities caused by the dynamic and labile nature of both the inorganic core and the organic-inorganic interface. Weak and dynamic binding between the NC surface and capping ligands causes rapid ligand desorption upon isolation and purification of colloids, eventually leading to a loss of structural integrity and sintering of NCs into bulk polycrystalline materials. Surface ligand engineering therefore remains an imminent research topic. Much progress in obtaining purifiable and stable colloids was achieved with a recent experimental discovery of new capping ligands, such as dimethyldidodecylammonium halides,[1,2] alkylphosphonic acids,[3] and long-chain zwitterionic ligands.[4] However, comprehensive understanding of the NC–ligand–solvent interface and the atomistic origins of the observed differences lags behind. In this study, we use classical molecular dynamics simulations to gain insights into the inherent binding properties of three different alkylammonium ligands – primary dodecylammonium (DA), secondary didodecylammonium (DDA) and quaternary dimethyldidodecylammonium (DMDDA) – in a mixture of nonpolar (toluene) and polar (acetone) solvents, the medium which is typically encountered during purification of the NCs. Our simulations uncover three main factors that govern effective ligand–substrate interactions: (i) the ability of the head-group to penetrate into the binding pocket, (ii) the strength of head-group's interactions with the polar solvent, and (iii) higher barrier for ligand adsorption/desorption in the case of multiple alkyl chains. The interplay between these factors causes the following order of the binding free energies: DDA < DA ≈ DMDDA, while surface capping with DDA and DMDDA ligands is additionally stabilized by the kinetic barrier. These findings are in agreement with experimental observations, wherein DDA is found to loosely bind to the CsPbBr₃ surface, while DMDDA capping is more stable than capping with primary oleylammonium ligand. The presented mechanistic understanding of the ligand-NC interactions is then used to design new cationic ligands that are expected to make perovskite NC surfaces more robust. We anticipate that the methodology, which is used in this study, can be extended to other types of inorganic materials with a predominantly noncovalent nature of interactions with capping ligands.