We present a study of carbon ion implantation in amorphous silica, which, followed by annealing in a hydrogen-rich environment, leads to preferential formation of carbon nanocrystals with cubic diamond (c-diamond), face-centered cubic (n-diamond), or simple cubic (i-carbon) carbon crystal lattices. Two different annealing treatments were used: furnace annealing for 1 h and rapid thermal annealing for a brief period, which enables monitoring of early nucleation events. The influence of implanted dose and annealing type on carbon and hydrogen concentrations, clustering, and bonding were investigated. Rutherford backscattering, elastic recoil detection analysis, infrared spectroscopy, transmission electron microscopy, selected area electron diffraction, ultraviolet-visible absorption measurements, and Raman spectroscopy were used to study these carbon formations. These results, combined with the results of previous investigations on similar systems, show that preferential formation of different carbon phases (diamond, n-diamond, or i-carbon) depends on implantation energy, implantation dose, and annealing conditions. Diamond nanocrystals formed at a relatively low carbon volume density are achieved by deeper implantation and/or lower implanted dose. Higher volume densities led to n-diamond and finally to i-carbon crystal formation. This observed behavior is related to damage sites induced by implantation. The optical properties of different carbon nanocrystal phases were significantly different.