In conservation biology, population monitoring is a critical step, particularly for endangered groups, such as steppe birds in European agro-ecosystems. Long-term population monitoring allows for determination of species population trends and also provides insights into the relative roles that environmental variability and human activities have on priority species. Here, we compare the population trends of two sympatric, closely related farmland bird species, the Little Bustard Tetrax tetrax and Great Bustard Otis tarda, in a protected area of Central Spain, which is their main stronghold in Europe. Over 12 years of monitoring, the abundance of Little and Great Bustards shifted in opposite directions in our study area. Little Bustard abundance decreased significantly (both males [-56%], and harder-to-detect females [-55%]), while Great Bustard abundance increased significantly (1,800%). Future surveys should be more precise and frequent for Little Bustards to facilitate evaluation of their population status and trends. We recommend annual surveys in 2–3 important locations by region throughout the breeding range for Little Bustards, while for Great Bustard the current regional monitoring programmes would be sufficient.