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Short-pulse ion beams have been developed in recent years and now enable applications in materials science. A tunable flux of selected ions delivered in pulses of a few nanoseconds can affect the balance of defect formation and dynamic annealing in materials. We report results from color center formation in silicon with pulses of 900 keV protons. G-centers in silicon are near-infrared photon emitters with emerging applications as single-photon sources and for spin-photon qubit integration. G-centers consist of a pair of substitutional carbon atoms and one silicon interstitial atom and are often formed by carbon ion implantation and thermal annealing. Here, we report on G-center formation with proton pulses in silicon samples that already contained carbon, without carbon ion implantation or thermal annealing. The number of G-centers formed per proton increased when we increased the pulse intensity from 6.9 × 109 to 7.9 × 1010 protons/cm2/pulse, demonstrating a flux effect on G-center formation efficiency. We observe a G-center ensemble linewidth of 0.1 nm (full width half maximum), narrower than previously reported. Pulsed ion beams can extend the parameter range available for fundamental studies of radiation-induced defects and the formation of color centers for spin-photon qubit applications.