The atomic structure of the aqueous glycine-fluorapatite (100) interface was investigated using grazing incidence X-ray diffraction. Experimental data analysis of crystal truncation rod intensities revealed detailed information on lateral as well as perpendicular ordering of the adsorbate molecules and the nature of atomic relaxations in the fluorapatite (FAp) (100) surface. Glycine and water molecules are arranged in two periodically ordered layers at the aqueous glycine-mineral interface. The adsorption process on the mineral surface is site competitive as both the glycine and water molecules show equal affinity toward surface Ca2+ cations. The glycine molecules interact directly with the FAp (100) surface, where one of their carboxylate groups coordinates with the surface Ca2+ cations. From the surface structure refinement, atomic positions of one glycine and four water molecules per unit cell were determined, along with the atomic relaxations in the FAp (100) surface. Molecular dynamic simulations were used to determine the long-range order of the adsorbate layers by investigating the hydrogen bonds.