Psittaciformes are among the most threatened birds, and population size and trend estimates are needed to aid conservation. The burrowing parrot Cyanoliseus patagonus is undergoing substantial changes in its population size, due to habitat degradation, trapping for the pet trade, and persecution as crop pest. The species formerly had several large colonies, but these were severely reduced during a programme of agricultural pest control. Currently, only one large colony remains, together with a decreasing number of smaller colonies spread throughout the Monte and adjacent ecoregions. The colony at El Cóndor, north‐eastern Patagonia, Argentina, is of particular importance, concentrating 71% of the global breeding population of burrowing parrots. We aimed to determine changes in 1) breeding population size, 2) the extent of the colony, 3) the distribution of nests along the colony, and 4) the timing of movements from the nest to the foraging locations during the breeding season, over our long‐term study (1998–2019). We found that the number of active nests declined from 37 531 in 2001 to 21 883 in 2005, and recovered in the following years, reaching 40 671 nests in 2019. The decline observed in 2005 could be related to droughts and associated food shortage during the La Niña phase of El Niño Southern Oscillation. The colony expanded westwards, from 9 km length in 2001, to 18.1 km in 2019. During the same period, the part of the colony with the highest number of active nests shifted 5 km westwards from El Cóndor village. Both changes could be the consequence of human disturbance. As any serious threat affecting this colony could have severe consequences for the survival of the species, regular monitoring is needed, together with legal protection of the burrowing parrot colony at El Cóndor and the Monte ecosystem around it.