Markham’s Storm Petrel Hydrobates markhami is endemic to the Humboldt Current, breeding inland in Chile and Peru. Its nesting habitat in Atacama Desert saltpeter deposits overlaps with light pollution, roadways, and other anthropogenic disturbances—factors that may impact the species’ populations. Owing to its remote nesting locations and nocturnal behavior, finding and monitoring its colonies is challenging. In fact, the first colonies were discovered only recently. In this study, we assessed whether passive acoustic monitoring of this species detects the same activity patterns as active nest monitoring. Acoustic monitors were placed at eight sites within colonies at Caleta Buena (Tarapacá Region) and Pampa Chaca (Arica Region), both located in the Atacama Desert, Chile. Acoustic data were processed with a trained Convolutional Neural Network detection model and analyzed to investigate diel and seasonal patterns. We then compared the call rates in areas with different burrow densities to assess this approach against active nest monitoring. We found that the mean call rate for each site was correlated with estimated nest densities. In both colonies, the seasonal pattern of vocal activity was similar to that reported in the literature based on active monitoring. This study also provides the first description of the species’ diel activity: birds of Caleta Buena became active between 102.9 ± 49.6 and 344.6 ± 47.9 min after sunset, and birds from Pampa Chaca were active between 86. 7 ± 23.0 and 187.2 ± 66.6 min after sunset. We conclude that passive acoustic monitoring may be effective for estimating the relative density of Markham’s Storm Petrel, especially in the early breeding season. Future monitoring in known colony areas should deploy recorders for longer periods to clarify breeding seasons and compare across colonies.