Lipid nanoparticles (LNPs) have emerged as a groundbreaking delivery system for vaccines and therapeutic mRNAs. Ionizable lipids are the most pivotal component of LNPs due to their ability to electrostatically interact with mRNA, allowing its encapsulation while concurrently enabling its endosomal escape following cellular internalization. Thus, extensive research has been performed to optimize the ionizable lipid structure and to develop formulations that are well tolerated and allow efficient targeting of different organs that result in a high and sustained mRNA expression. However, one facet of the ionizable lipids’ structure has been mostly overlooked: the linker segment between the ionizable headgroup and their tails. Here, we screened a rationally designed library of ionizable lipids with different biodegradable linkers. We extensively characterized LNPs formulated using these ionizable lipids and elucidated how these minor structural changes in the ionizable lipids structure radically influenced the LNPs’ biodistribution in vivo. We showed how the use of amide and urea linkers can modulate the LNPs’ pKa, resulting in an improved specificity for lung transfection. Finally, we demonstrated how one of these lipids (lipid 35) that form LNPs entrapping a bacterial toxin [pseudomonas exotoxin A (mmPE)] in the form of an mRNA reduced tumor burden and significantly increased the survival of mice with lung metastasis.