Abstract Chenopodium quinoa Willd. (quinoa) is a pseudocereal with high nutritional value and relatively high tolerance to several abiotic stresses, including water deficiency and salt stress, making it a suitable plant for the study of mechanisms of abiotic stress tolerance. NAC (NAM, ATAF and CUC) transcription factors are involved in a range of plant developmental processes and in the response of plants to biotic and abiotic stresses. In the present study, we perform a genome-wide comprehensive analysis of the NAC transcription factor gene family in quinoa. In total, we identified 107 quinoa NAC transcription factor genes, distributed equally between sub-genomes A and B. They are phylogenetically clustered into two major groups and 18 subgroups. Almost 75% of the identified CqNAC genes were duplicated two to seven times and the remaining 25% of the CqNAC genes were found as a single copy. We analysed the transcriptional responses of the identified quinoa NAC TF genes in response to various abiotic stresses. The transcriptomic data revealed 28 stress responsive CqNAC genes, where their expression significantly changed in response to one or more abiotic stresses, including salt, water deficiency, heat and phosphate starvation. Among these stress responsive NACs, some were previously known to be stress responsive in other species, indicating their potentially conserved function in response to abiotic stress across plant species. Six genes were differentially expressed specifically in response to phosphate starvation but not to other stresses, and these genes may play a role in controlling plant responses to phosphate deficiency. These results provide insights into quinoa NACs that could be used in the future for genetic engineering or molecular breeding.