The procedures of putrescine, spermine, spermidine, and cadaverine derivatization using 2-chloro-1,3-dinitro-5-(trifluoromethyl)benzene, 1-fluoro-2-nitro-4-(trifluoromethyl) benzene, and 3,5-bis-(trifluoromethyl)phenyl isothiocyanate for chromatographic determination in home-made wine samples are compared in the present study. The procedures discussed were compared regarding simplicity, linearity, precision, and accuracy. The polyamines derivatives were isolated and characterized by X-ray crystallography and 1H, 13C, and 19F NMR spectroscopy. The obtained structures of aliphatic amines showed that all amino groups, four in spermine, two in putrescine and cadaverine, and three in spermidine, regardless of the applied reagent, were substituted. The applicability of the described procedures was tested during the chromatographic analysis of the compounds’ content in home-made wines. For this purpose, a simple and environmentally friendly sample preparation procedure was developed. The obtained results present the derivatization of polyamines with 1-fluoro-2-nitro-4-(trifluoromethyl)benzene as a better choice for the determination of these compounds in food samples.