Methotrexate (MTX), a compound originally used as an anticancer drug, has also found applications in a broad variety of autoimmune disorders thanks to its anti-inflammation and immunomodulatory functions. The broad application of MTX is anyway limited by its poor solubility in biological fluids, its poor bioavailability and its toxicity. In addition, encapsulating its original form in nanoformulation is very arduous due to its considerable hydrophobicity. In this work, two strategies to efficiently encapsulate MTX into liposomal particles are proposed to overcome the limitations mentioned above and to improve MTX bioavailability. MTX solubility was increased by conjugating the molecule to two different compounds: DSPE and PEG. These two compounds commonly enrich liposome formulations, and their encapsulation efficiency is very high. By using these two prodrugs (DSPE-MTX and PEG-MTX), we were able to generate liposomes comprising one or both of them and characterized their physiochemical features and their toxicity in primary macrophages. These formulations represent an initial step to the development of targeted liposomes or particles, which can be tailored for the specific application MTX is used for (cancer, autoimmune disease or others).