Interest in lipid-based lyotropic liquid crystalline nanoparticles (LCNPs) as drug delivery vehicles continues to grow, owing to their unique structural features. The structure of these particles can be controlled to suit specific applications, through tailoring the lipid composition and solvent conditions. Ionic liquids (ILs) are liquid salts comprising tailorable cations and anions, of which some are known to support the self-assembly of amphiphiles, and hence can be used as designer solvents for LCNPs. We employed dynamic light scattering, small angle X-ray scattering, and cryogenic transmission electron microscopy to examine the particle size and lyotropic liquid crystalline mesophase behavior of monoolein (MO)-based LCNPs in aqueous solutions containing 13 choline ILs with a selection of amino acid and carboxylate anions at 6 concentrations 20, 10, 5, 1, 0.33, and 0.16 wt%. Our results show the formation of LCNPs with various liquid crystalline nanostructures, including the inverse bicontinuous primitive cubic (Q2) phase with the Im3m crystallographic space group, the inverse hexagonal (H2), and the inverse discontinuous micellar cubic (I2) phases. The internal nanostructures of the MO nanoparticles depended on three main factors, the anion of the ILs, the IL concentration, and the pH of the solution. This study elucidates the potential application of IL solvents as a powerful tool to tailor the internal nanostructure of MO-based LCNPs, and advances the exploration of IL-enabled responsive LCNPs systems as prospective nanocarriers.