X-ray fluorescence CT (XFCT) has shown promise for molecular imaging of gold nanoparticles. To date, XFCT has been induced by kilovoltage photon beams due to the high photoelectric interaction probability. We compare K-shell and L-shell XFCT induced by photon, electron, and proton beams for two phantom sizes. A 2.5 and 5.0-cm diameter phantom with four 5 mm and 10 mm vials, respectively, with gold-solutions of 0.1%-2% by weight were built in TOPAS, a GEANT4-based Monte Carlo simulation tool. The 2.5-cm phantom was imaged with XFCT induced by beams of 7.45×104 81 keV- and 5 MeV-photons, 220 kVp- and 6 MV-photons, 10 MeV- and 100 MeV-electrons, and 100 MeV- and 250 MeV-protons. The doses between each phantom size were equal. First-generation CT geometry with 0.5 mm × 0.5 mm pencil beams with 0.5 mm-translation and 2°-rotation steps over each phantom was modeled. The scattered x-rays were detected on an idealized spherical detector from which the K-shell and L-shell fluorescent x-rays were extracted in 0.5 keV and 0.2 keV bins. XFCT images were generated using iterative reconstruction algorithms. The highest gold sensitivity was seen in the 81 keV-photon K-shell and L-shell images (0.004% and 0.007%) of the 5.0 cm-phantom at 30 mGy. For the 2.5 cm-phantom, the detection limits were 0.006%, 0.62%, and 0.28% for 81 keV-photon K-shell, 100 MeV-electron K-shell, and 100 MeV-proton L-shell images, respectively. The mean imaging dose was approximately 2-3 orders of magnitude higher in electron- and proton-XFCT compared to 81keV-photon XFCT. Our MC study demonstrates that the small-object XFCT imaging achieves the best performance when induced with kilovoltage-photon beams. Due to high imaging doses, electron- and proton-induced XFCT might be feasible for guiding nanoparticle-enhanced charged-particle radiotherapy.