Dual Energy (DE) imaging has been widely used in digital radiography and fluoroscopy, as has dual energy CT for various medical applications. In this study, the imaging performance of a dynamic dual-layer a-Si flat panel detector (FPD) prototype was characterized for dual energy imaging tasks. Dual energy cone beam CT (DE CBCT) scans were acquired and used to perform material decomposition in the projection domain, followed by reconstruction to generate material specific and virtual monoenergetic (VM) images. The dual-layer FPD prototype was built on a Varex XRD 4343RF detector by adding a 200 μm thick CsI scintillator and a-Si panel of 150 μm pixel size on top as a low energy detector. A 1 mm copper filter was added as a middle layer to increase energy separation with the bottom layer as a high energy detector. The imaging performance, such as Modulation Transfer Function (MTF), Conversion Factor (CF), and Detector Quantum Efficiency (DQE) of both the top and bottom detector layers were characterized and compared with those of the standard single layer XRD4343 RF detector. Several tissue equivalent cylinders (solid water, liquid water, bone, acrylic, polyethylene, etc.) were placed on a rotating stand, and two separate 450-projection CBCT scans were performed under continuous 120 kV and 80 kV X-ray beams. After an empirical material decomposition calibration, water and bone images were generated for each projection, and their respective volumes were reconstructed using Varex’s CBCT Software Tools (CST 2.0). A VM image, which maximized the contrast-to-noise ratio of water to polyethylene, was generated based on the water and bone images. The MTF at 1.0 lp/mm from the low energy detector was 32% and 22% higher than the high energy detector and the standard detector, respectively; the DQE of both high and low energy detectors is much lower than that of the standard XRD 4343RF detector. The CNR of water to polyethylene from the VM image improved by 50% over that from the low energy image alone at 120 kV, and by 80% at 80 kV. This study demonstrates the feasibility of using a dual-layer FPD in applications such as DE CBCT for contrast enhancement and material decomposition. Further evaluations are underway.