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Accurate long-term monitoring of a threatened species’ population size and trend is important for conservation management. The endangered yellow-eyed penguin (Megadyptes antipodes) is a non-colonial breeder. Population monitoring of the subantarctic population has focused on beach counts rather than nesting birds. Here, we combined intensive nest-searching and counts of transiting penguins on Enderby Island, Auckland Islands, over 3 years to establish the relationship between count numbers and breeding birds. Morning beach counts of transiting penguins were extrapolated to estimate breeding population for the entire Auckland Island group from 2012 to 2017. Breeding numbers varied considerably between years, but overall did not appear to be declining in the short term. Breeding birds at the Auckland Islands averaged 577 pairs annually over the three ground-truthed breeding seasons, similar to the lower estimate of 520–680 pairs from the last survey in 1989, but less than the higher estimate of 650–1,009 pairs generated from that survey. Direct comparison of beach counts indicated a large decline, but these may be more prone to uncertainty. Large variations between years indicated variable breeding effort. The Auckland Islands (particularly Enderby Island) represent 37–49% of the total breeding population for yellow-eyed penguins, indicating the importance of the subantarctic populations for the species. We recommend ongoing monitoring, including mark-recapture methods, for future population estimates. At least 50% of the individuals in an area should be marked to reduce confidence intervals of estimates.