Organisms exhibit the ability to achieve precise spatial and temporal patterning of crystalline units during the growth of biominerals. A key feature of those biominerals is their nanocomposite structure. Several biominerals, such as sea urchin teeth and mollusk shells have encapsulated nanoparticles within large single mesostructured crystals. Due to their unique nanocomposite structure, biogenic minerals exhibit superior strength, hardness, and toughness compared to their geological counterparts (e.g. the sea urchin using its calcitic teeth to grind calcitic limestone) and remarkable optical properties (e.g. the iridescence of mollusk shells). Incorporating guest nanoparticles within inorganic single crystals opens the door to the creation of new nanocomposites, and understanding the mechanisms of incorporation can lead to a new science of nanocomposites with tunable properties. We investigate the influence of surface chemistry on the incorporation of nanoparticles in calcite crystals. How is chemical information transferred from the nanoparticle across an interface to the growing inorganic material? Can we engineer the interface energy landscape to guide the incorporation of nanoparticles? We report successful incorporation of sub-10 nm fluorescent silica nanoparticles in calcite crystals. We use a combination of silane and click chemistry to decorate the surface of fluorescent silica nanoparticles with carboxyl or hydroxyl groups. By introducing different fluorescent dyes into the cores of the silica nanoparticles, we create “bar-coded” nanoparticle in which the surface chemistry is tagged by a specific dye, i.e., the fluorescent nanoparticles have different emission wavelengths depending on their surface chemistries. We demonstrate that by growing calcite crystals in the presence of nanoparticles with two different surface chemistries tagged by different dyes, we can observe the influence of surface chemistry on the incorporation of nanoparticles. We use laser-scanning confocal microscopy to visualize the 3D distribution of the different color nanoparticles within the calcite crystals. Our findings show that decorating silica nanoparticles with 0.49 hydroxyl groups per nm2 of nanoparticle surface increased their incorporation in calcite crystals by more than twofold, and decorating them with the same amount of carboxyl groups multiplied their incorporation by almost three times and a half. However, a lower density of surface functionalization (0.13/nm2) did not result in any improvement, whether it were hydroxyl or carboxyl groups. This work presents a model for studying how the surface chemistry, size and morphology of nanoparticles influences the pattern of incorporation within growing crystals.