The formation of dipeptide micro- and nanostructures in the solid state or in solutions usually occurs in the presence of water in the ambient air or in the organic media used. This factor should be taken into account since the results of the self-assembly of dipeptides are very sensitive to external conditions and may depend on the water content. In this work, the study of the mutual effect of water and organic vapors on the self-assembly of the glycyl-glycine (GlyGly) dipeptide in the solid state was carried out for the first time using atomic force microscopy. The crystallization of an amorphous GlyGly film upon interaction with vapors of organic compounds such as dichloromethane, chloroform, tetrachloromethane, and benzene occurs only in the presence of water vapors. The rate of dipeptide crystallization was found also depends on the organic compound used. The solubility of GlyGly in organic media and the solubility of organic solvent in water are the main factors that affect the dipeptide self-assembly. Using the Raman spectroscopy and quantum chemical calculations a possible mechanism of the combined effect of water and organic compounds on the GlyGly self-assembly has been proposed.