Conventional X-ray computed tomography (CT) systems obtain single- or dual-energy measurements, from which dual-energy CT has emerged as the superior way to recognize materials. Recently photon counting detectors have facilitated multi-spectral CT which captures spectral information by counting photon arrivals at different energy windows. However, the narrow energy bins result in a lower signal-to-noise ratio in each bin, particularly in the lower energy bins. This effect is significant and challenging when high-attenuation materials such as metal are present in the area to be imaged. In this paper, we propose a novel technique to estimate material properties with multi-spectral CT in the presence of high-attenuation materials. Our approach combines basis decomposition concepts using multiple-spectral bin information, as well as individual energy bin reconstructions. We show that this approach is robust in the presence of metal and outperforms alternative techniques for material estimation with multi-spectral CT as well with the state-of-art dual-energy CT.