VYXEOS® is the first FDA-approved dual-API liposomal formulation containing two different chemotherapeutics, daunorubicin and cytarabine at a 1:5 molar ratio. Analysis of bulk formulation does not provide insight to size-based distribution of APIs and excipients, therefore asymmetrical flow field-flow fractionation (AF4) was utilized for the size-based separation of VYXEOS® liposomes and collected size fractions were further analyzed for the concentrations of APIs, lipid excipients, and copper. Analysis results revealed a significant variation in API distribution across the size fractions, with the larger liposomes encapsulating a higher ratio of cytarabine to daunorubicin compared to the smaller liposomes, while lipid excipient composition was held constant across the size range. We attribute the size-based variation of API ratios to structural change during API loading and sequence of API loading. Cytarabine is first passively loaded into liposomes containing copper gluconate, and then daunorubicin is actively loaded using copper gradient where the daunorubicin is retained in the liposomes as a copper complex. This method can be extended to characterize various single and dual-API liposomal nanocarriers during drug product development and/or post market quality control.