Quinoa (Chenopodium quinoa Willd.) is an ancestral crop in the Ecuadorian Andean region, and its landraces have always been of great social and food importance for the native population. Currently, there is no updated information about their phenotypic diversity and conservation status nor about the changes that have occurred in the last decades. A total of 268 accessions of quinoa landraces collected at two different times (1978–1988 and 2014–2015) in three representative Ecuadorian Andean provinces (Imbabura, Cotopaxi and Chimborazo) were evaluated for forty agro-morphological (17 quantitative and 23 qualitative) traits. Most of the quantitative traits showed high variability, some of them with great importance for commercialization and germplasm selection for breeding programs (e.g., panicle width, grain width, 1000-grain weight or seed yield per plant). Ten quantitative and eleven qualitative descriptors were significantly different between both collections. Regarding the presence/absence of saponin, all the accessions collected four decades ago had saponin, while it was found in only 18% of accessions collected more recently. The phenotypic relationships in the dendrogram did not show clustered accessions by their geographical origin or by collection. A selection index allowed us to detect a few accessions recently collected in Chimborazo with high promises for future breeding programs, with high seed yields per plant values and a reduced or no saponin content. The agro-morphological information obtained may be very useful for the suitable management and conservation of this ancestral plant genetic resource, both on the farm by indigenous farming communities and ex situ by the Germplasm Bank of the Ecuadorian National Institute for Agricultural Research (INIAP).