At subduction zones, most diamonds form by carbon saturation in hydrous fluids released from lithospheric plates on equilibration with mantle rocks. Although organic molecules are predicted among dissolved species which are the source for carbon in diamonds, their occurrence is not demonstrated in nature, and the physical model for crustal diamond formation is debated. Here, using Raman microspectroscopy, I determine the structure of carbon-based phases inside fluid inclusions in diamond-bearing rocks from the Alps. The results provide direct evidence that diamond surfaces are coated by sp2-, and sp3-bonded amorphous carbon and functional groups of carboxylic acids (e.g., carboxyl, carboxylate, methyl, and methylene), indicating the geosynthesis of organic compounds in deep hydrous fluids. Moreover, this study suggests diamond nucleation via metastable molecular precursors. As a possible scenario, with carbon saturation by reduction of carboxylate groups, I consider tetrahedral H-terminated C groups as templates for the growth of sp3-structured carbon.