A method for preparing a phospholipid delivery system encapsulating one or more bio-affecting compounds, includes the steps of solubilizing a heterogeneous phospholipid mixture into an organic solvent to form a concentrated formulation of phospholipids, in which the phospholipids include a charged phospholipid species and mixing the concentrated formulation with an aqueous solution having at least one bio-affecting compound. A method of using a phospholipid delivery system encapsulating at least one bio-affecting compound for the administration to an individual in need thereof is also disclosed.