Supramolecular organic systems can be used as a host for the encapsulation of small organic molecules. Here, we chose melamine barbiturate as a robust system capable of supramolecular assembly and the Rhodamine 6G dye entrapment as a guest molecule. The encapsulation of the dye was investigated by UV-visible spectroscopy, SEM and optical fluorescent microscopy while the insight into the crystal structure of the system was obtained by single crystal and powder XRD. For investigation of the system’s properties on a molecular level, the DFT and Classical Molecular Dynamics methods were utilized. Surprisingly, both theoretical and experimental data show not only the successful encapsulation of Rhodamine 6G molecules inside the supramolecular assembly, but also that inclusion of such molecules leads to the drastic improvement in the organic crystal shape. The melamine barbiturate in presence of the Rhodamine 6G molecules tend to form crystals with lesser degree of twinning and higher symmetry in shape than the ones without dye molecules.