Dual-energy (DE) decomposition has been adopted in orthopedic imaging to measure bone composition and visualize intraarticular contrast enhancement. One of the potential applications involves monitoring of callus mineralization for longitudinal assessment of fracture healing. However, fracture repair usually involves internal fixation hardware that can generate significant artifacts in reconstructed images. To address this challenge, we develop a novel algorithm that combines simultaneous reconstruction-decomposition using a previously reported method for Model-Based Material Decomposition (MBMD) augmented by the Known-Component (KC) reconstruction framework to mitigate metal artifacts. We apply the proposed algorithm to simulated DE data representative of a dedicated extremity cone-beam CT (CBCT) employing an x-ray unit with three vertically arranged sources. The scanner generates DE data with non-coinciding high- and low-energy projection rays when the central source is operated at high tube potential and the peripheral sources at low potential. The proposed algorithm was validated using a digital extremity phantom containing varying concentrations of Ca-water mixtures and Ti implants. Decomposition accuracy was compared to MBMD without the KC model. The proposed method suppressed metal artifacts and yielded estimated Ca concentrations that approached the reconstructions of an implant-free phantom for most mixture regions. In the vicinity of simple components, the errors of Ca density estimates obtained by incorporating KC in MBMD were ~1.5 – 5x lower than the errors of conventional MBMD; for cases with complex implants, the errors were ~3 – 5x lower. In conclusion, the proposed method can achieve accurate bone mineral density measurements in the presence of metal implants using non-coinciding DE projections acquired on a multisource CBCT system.© 2020 Institute of Physics and Engineering in Medicine.