The complete structure of non-crystalline compounds can be determined by confining them in crystalline structures. The reduced motional degrees of freedom of encapsulated guests can be obtained through their anchoring to the host cages, which results in the reduction of a significant amount of disorder. The "pyrene box" cages that easily crystallize from aqueous solutions are recommended to achieve complete structure elucidation of compounds of biological interest. In this study, the "pyrene box" cages have been used for the in situ encapsulation of biogenic amines: histamine, dopamine, and serotonin. NMR spectroscopy illustrates that these systems are stable in aqueous solution. The X-ray single-crystal structure analysis reveals that the pyrene box/biogenic amine systems are stabilized through combined interactions, strongly contributing to in situ fixation and accurate determination of their crystal structures.