In targeted drug delivery systems, it is desirable that the delivery of hydrophobic drugs to a cell or tissue is achieved with little to no side effects. To ensure that the drugs do not leak during circulation, encapsulation stability of the drug carrier in serum is critical. In this paper, we report on a modified FRET-based method to evaluate encapsulation stability of amphiphilic assemblies and cross-linked polymer assemblies in serum. Our results show that serum components can act as reservoirs for hydrophobic molecules. We also show that serum albumin is likely to be the primary determinant of this property. This work highlights the importance of assessing encapsulation stability in terms of dynamics of guest molecules, as it provides the critical distinction between hydrophobic molecules bound inside amphiphilic assemblies and the molecules that are bound to the hydrophobic pockets of serum albumin.