The preferential incorporation of carboxylic acids into aragonite and its effects on the crystal growth and physicochemical properties of aragonite were systematically investigated using a seeded co-precipitation system with different carboxylic acids (citric, malic, acetic, glutamic, and phthalic). Aragonite synthesized in the presence of citric and malic acids showed a remarkable decrease in the crystallinity and size of crystallite, and the retardation of crystal growth distinctively changed the crystal morphology. The contents of citric acid and malic acid in the aragonite samples were 0.65 wt % and 0.19 wt %, respectively, revealing that the changes in the physicochemical properties of aragonite were due to the preferential incorporation of such carboxylic acids. Speciation modeling further confirmed that citric acid with three carboxyl groups dominantly existed as a metal–ligand, (Ca–citrate)−, which could have a strong affinity toward the partially positively charged surface of aragonite. This indicates why citric acid was most favorably incorporated among other carboxylic acids. Our results demonstrate that the number of carboxyl functional groups strongly affects the preferential incorporation of carboxylic acids into aragonite; however, it could be suppressed by the presence of other functional groups or the structural complexity of organic molecules.