To investigate value of spectral reconstructions for the quantification of coronary stenosis in the presence of calcified or partially calcified plaques using a dual-layer spectral detector CT (SDCT). Seventy-two consecutive patients were retrospectively enrolled. Conventional 120 kVp images, eight virtual monoenergetic images (VMI) (70 to 140 keV), the effective atomic number (Z effective) and iodine no water images were reconstructed. Invasive coronary angiography was used as the reference standard. Parallel and serial testing were used to assess the incremental diagnostic value of Z effective and iodine no water images to the best VMI series. 122 coronary lesions of 72 patients (49 men and 23 women; 63.7 ± 10.2 years) were enrolled in analysis. Reconstruction at 100 keV yielded optimal diagnostic performance, the sensitivity, specificity, PPV, NPV and diagnostic accuracy to identify stenosis ≥ 50% or ≥ 70% were 84%, 70%, 80%, 76%, 79% and 78%, 98%, 93%, 91%, 92%, respectively. A serial combination (100 keV VMI followed by Z effective images) resulted in an improved specificity (from 70 to 80%) with a moderate loss of sensitivity (81% from 84%) in identifying ≥ 50% stenosis (P = 0.021). For patients with high Agatston score, this combination could further reduce false positive cases and improve diagnostic accuracy. 100 keV VMI provide optimal diagnostic performance for the detection of coronary stenosis in the presence of calcified or partially calcified plaques using a dual-layer SDCT, with further improvements obtained with the combined use of Z effective images.