Abstract Pyrene boxes, self‐assembled from 1,3,5,8‐pyrene‐tetrasulfonate anions, PTS 4− and Guanidinium G + , amino‐guanidinium AG + and hydrated alkali counter cations have been used for the encapsulation of 1,ω‐amino‐acids of variable lengths. The NMR spectroscopy illustrates that these systems are stable in aqueous solution and encapsulation process involves dynamic or fixed guest molecules within Pyrene box, depending of the nature of the counter‐cations. The amide bond coupling between the amino‐guanidinium AG + and encapsulated 1,ω‐amino‐acid guests occur in water in the absence of coupling catalysts. The variable co‐encapsulation of the guests via multivalent stabilizing interactions shed light that chemical selection can be obtained from mixtures of 1,ω‐amino‐acids. Our study involving a comprehensive screening of 18 co‐crystal structures help to understand the in‐situ fixation of 1,ω‐amino‐acid guests and their accurate determination of unconventional structures under confinement.