The success of COVID-19 mRNA vaccines has drawn significant interest in developing lipid nanoparticles (LNPs) for gene delivery. Traditional LNP formulations employing polyethylene glycol-based stabilizers have been associated with potential limitations such as immunogenicity and accelerated clearance upon repeated administration. This study introduces LNPs incorporating choline-based ionic liquids (ILs) instead of PEGylated stabilizers for mRNA delivery, particularly to transfect alveolar macrophages. We systematically investigated LNPs incorporated with three choline-based ILs (choline hexanoate, choline aspartate and choline glutamate) including their physicochemical properties, stability and in vitro biological performance. It was found that ILs with amino acid anions, such as aspartate and glutamate, could lead to relatively stable LNP formulations in the absence of PEGylated stabilizers. These IL-incorporated LNPs exhibited notably improved intracellular mRNA transfection in alveolar macrophages compared to copolymer F127-stabilized LNPs. We revealed acidification-induced structural transitions into more ordered inverse lipid mesophases of IL-incorporated LNPs, which may facilitate endosomal escape and efficient mRNA transfection. This LNP property-biological performance relationship study provides valuable insights into designing next-generation nanocarriers for gene delivery. The incorporation of ILs offers a promising avenue to modify the property and performance of LNPs for nanomedicine and mRNA vaccines. This article is part of the discussion meeting issue 'Ionic liquids and the future of soft materials'.