Lipid-based drug delivery systems (DDS) have attracted considerable interest for their capacity to achieve controlled drug release and encapsulate a variety of drug molecules—hydrophobic, hydrophilic, and amphiphilic—enabling diverse therapeutic applications. The research focuses on the structural and functional aspects of lipid-based vesicles that encapsulate both anti-cancer and anti-microbial drugs. The study employs ultrasensitive isothermal titration calorimetry and differential scanning calorimetry to gain mechanistic insights into the partitioning of drugs in the lipid-based DDS, release mechanisms, and binding interactions with serum proteins after the release.The structural properties of 5-fluorouracil (5-FU) suggest that the drug can partition into the outer region of the bilayer, where it forms hydrogen bonds with the polar heads of the amphiphilic lipid chains. Kanamycin indicates strong partitioning into liposomes as it displays a binding constant of the order of 106. Erythromycin exhibits limited partitioning into the bilayer, as assessed by fitting ITC data using a sequential two-binding site model. The values of change in enthalpy and entropy reflect the interaction nature and desolvation process during the drug's partitioning into liposomes. Thermodynamic signatures and transition temperatures obtained from ITC and DSC studies indicate that no diffusion-based drug release occurs from DPPC and DSPC-based liposomes. The interaction heat between the released drug and carrier serum albumin protein is very low and shows no consistent pattern. This suggests that the drugs are stably encapsulated in the drug delivery system (DDS), with no significant leakage over time. Insights from such studies on the influence of drug molecule structure on its partitioning into various lipid vesicles and further release of the same drugs from it guide in criteria for developing improvised drug delivery systems.