Since 1994, IUCN Red List assessments apply globally acknowledged standards to assess species distribution, abundance and trends. The extinction risk of a species has a major impact on conservation science and international funding mechanisms. Great ape species are listed as Endangered or Critically Endangered. Their populations are often assessed using their unique habit of constructing sleeping platforms, called nests. As nests rather than apes are counted, it is necessary to know the time it takes for nests to disappear to convert nest counts into ape numbers. However, nest decomposition is highly variable across sites and time and the factors involved are poorly understood. Here, we used 1,511 bonobo (Pan paniscus) nests and 15 years of climatic data (2003–2018) from the research site LuiKotale, Democratic Republic of the Congo, to investigate the effects of climate change and behavioural factors on nest decay time, using a Bayesian gamma survival model. We also tested the logistic regression method, a recommended time-efficient option for estimating nest decay time. Our climatic data showed a decreasing trend in precipitation across the 15 years of study. We found bonobo nests to have longer decay times in recent years. While the number of storms was the main factor driving nest decay time, nest construction type and tree species used were also important. We also found evidence for bonobo nesting behaviour being adapted to climatic conditions, namely strengthening the nest structure in response to unpredictable, harsh precipitation. By highlighting methodological caveats, we show that logistic regression is effective in estimating nest decay time under certain conditions. Our study reveals the impact of climate change on nest decay time in a tropical remote area. Failure to account for these changes would invalidate biomonitoring estimates of global significance, and subsequently jeopardize the conservation of great apes in the wild.