Mineralized tissues grow through biologically controlled processes in which specific macromolecules are involved. Some of these molecules, which are present in very low concentrations and are difficult to localize and characterize, become entrapped inside the mineralized tissue. Herein, a protein fragment, GP, which was obtained by the alkaline digestion of the green sheet of the abalone shell, is used as a probe to study the changes in molecular structure that occur during the precipitation of calcium carbonate. This important goal was achieved by exploiting a fluorescent tag in GP. The experimental results that were obtained by using spectroscopic-, chromatographic-, and microscopic techniques indicate that GP controls the precipitation kinetics and morphology of calcium carbonate crystals, and that it only undergoes structural reorganization when entrapped inside calcium carbonate crystals. To the best of our knowledge, this report represents one of the first studies on the conformational changes of a protein fragment that is involved in biomineralization processes on moving from the solution phase into the mineral phase.