Autoimmune diseases are a major health concern in developed countries. Currently, only palliative treatments based on anti-inflammatories and immunosuppressors are available. A novel antigen-specific therapy that uses a physiological process of tolerance generation is being developed. This is plausible by using phosphatidylserine rich liposomes (PS-liposomes), which bio-mimic apoptotic cells, encapsulated with the autoantigen responsible of generating the autoimmunity. In this way, tolerance against the own cells or tissues that were considered hostile can be achieved. In addition, only by changing the encapsulated peptide, different autoimmune diseases can be treated. Efficacy of this approach was demonstrated in type I diabetes, rheumatoid arthritis, multiple sclerosis, and myasthenia gravis.In the regulatory pre-clinical phase, analytical methodologies to evaluate the quality of the product need to be developed. In this regard, identification and quantification of the encapsulated peptide and lipids are considered critical quality attributes. In this study, a rapid and simple liquid–liquid extraction procedure, based on Bligh-Dyer method, is described for dual extraction of peptides and lipids within PS-liposomes formulation. This single step allows the separation of lipids and the encapsulated peptide in two different phases. For the subsequent analysis, two different HPLC methods were developed. The organic phase, which contains the lipids was analysed by HPLC-ELSD, while the aqueous phase, containing the encapsulated peptide, was analysed by HPLC-UV. Both methods were also validated in terms of accuracy, precision, linearity, LOD and LOQ. The extraction procedure has demonstrated highly efficient separation of lipids and peptides, avoiding interferences between them in the quantification.