Abstract Background Nuclear magnetic resonance spectroscopy is one of the primary tools in metabolomics analyses, where it is used to track and quantify changes in metabolite concentrations or profiles in response to perturbation through disease, toxicants or drugs. The spectra generated through such analyses are typically confounded by noise of various types, obscuring the signals and hindering downstream statistical analysis. Such issues are becoming increasingly significant as greater numbers of large-scale systems or longitudinal studies are being performed, in which many spectra from different conditions need to be compared simultaneously. Results We describe a novel approach, termed Progressive Consensus Alignment of Nmr Spectra (PCANS), for the alignment of NMR spectra. Through the progressive integration of many pairwise comparisons, this approach generates a single consensus spectrum as an output that is then used to adjust the chemical shift positions of the peaks from the original input spectra to their final aligned positions. We characterize the performance of PCANS by aligning simulated NMR spectra, which have been provided with user-defined amounts of chemical shift variation as well as inter-group differences as would be observed in control-treatment applications. Moreover, we demonstrate how our method provides better performance than either template-based alignment or binning. Finally, we further evaluate this approach in the alignment of real mouse urine spectra and demonstrate its ability to improve downstream PCA and PLS analyses. Conclusions By avoiding the use of a template or reference spectrum, PCANS allows for the creation of a consensus spectrum that enhances the signals within the spectra while maintaining sample-specific features. This approach is of greatest benefit when complex samples are being analyzed and where it is expected that there will be spectral features unique and/or strongly different between subgroups within the samples. Furthermore, this approach can be potentially applied to the alignment of any data having spectra-like properties.