In this work, an energy-resolving thermoelectrically cooled single crystal cadmium telluride (CdTe) detector system upgraded with the latest firmware was optimized for high X-ray flux operations using high bias voltage and fast peaking time. This detector system was deployed into an experimental benchtop X-ray fluorescence (XRF) imaging/computed tomography (XFCT) system developed for quantitative imaging of metal nanoprobes such as gold nanoparticles (GNPs). Using the firmware-upgraded and existing/old CdTe detector systems, the Compton/XRF spectra from small (8 mm diameter) GNP-containing phantoms were acquired. The phantoms were irradiated with 1.8 mm Sn-filtered 125 kVp cone beam X-rays at 24 mA. The firmware-upgraded detector system produced relatively lower dead time under high X-ray flux, compared with the old detector system, and performed well with the spectral resolution of ∼0.7 keV (in full width at half maximum) at 69 keV photon energy. Given the same 2 mm aperture detector collimator and irradiation time of 10 s, this detector system managed to score nearly 50% more gold XRF signals than the existing one at all GNP concentrations tested. This improvement resulted in the GNP detection limit of 0.02 wt. % which was lower than that (0.03 wt. %) achievable with the existing detector system. When combined with the detector collimator containing a larger (3 mm) aperture, the firmware-upgraded detector system produced drastically more gold XRF signal at a given GNP concentration (e.g., 9 times more for 1 wt. % GNP solution and irradiation time of 10 s), leading to further reduction in the GNP detection limit (i.e., 0.01 wt. %). The present investigation showed that the firmware upgraded CdTe detector system optimized for high X-ray flux operations allowed for better photon counting efficiency, thus leading to sensitivity enhancement of an experimental benchtop XRF/XFCT imaging system.