Crystalline proteins may offer superior properties for drug delivery compared to standard protein formulations such as aqueous solutions or amorphous precipitated lyophilisates. In this study, a new approach using biocompatible, hydrophilic, substituted alkylammonium-based ionic liquids (ILs) as additives for the advanced crystallization of two exemplary proteins, lysozyme and lipase, was investigated. Sitting-drop vapor diffusion crystallization experiments revealed that the addition of some of the ILs resulted in less crystal polymorphism and precipitation was consistently avoided, even at larger concentrations of the conventional crystallization agent. The kinetics of lysozyme crystallization were significantly enhanced by a factor of up to 5.5 using ILs with strongly hydrated anions, i.e., formate or glycolate. In contrast, ILs with weakly hydrated anions, i.e., nitrate, led to undesirable spontaneous precipitation. In addition, lipase was crystallized preferentially using an IL with a strongly hydrated anion, i.e. dihydrogenphosphate. Large, sturdy crystals were formed at rates which were enhanced by a factor of up to 4.