This study investigated the effect of noncommon ions on the phase transformation of guanosine 5-monophosphate disodium (GMP disodium salt, Na(2)GMP) in the case of antisolvent crystallization. Thus, GMP was synthesized by biological fermentation and then purified by antisolvent crystallization, which included the phase transformation of the amorphous phase of GMP disodium salt into the crystalline phase via a recrystallization process in the solution. However, during this phase transformation, the addition of K+ and Ca2+ as noncommon ions had a significant impact as they were popular ionic impurities in the fermented solution. Thus, the Na+ ions in the GMP disodium salt were replaced with K+ and Ca2+ ions to form new amorphous GMP complex salts, such as Na/K.GMP or Na/Ca.GMP. The solid structures of these amorphous GMP complex salts were much more stable than the solid structures of the amorphous and crystalline GMP disodium salt, meaning that the solubility of the GMP complex salts in the solvent was much lower than the solubility of the GMP disodium salt. In addition, the replacement of the Na+ ions in the GMP disodium salt with K+ and Ca2+ ions inhibited the formation and ordered-stacking of the GMP G-quartets. Thus, the amorphous GMP complex salts did not transform into a crystalline phase. This impact of the K+ and Ca2+ ions was confirmed by element mapping images and the element ratios in the GMP complex salts.