The Little Bustard is suffering a widespread population decline mainly due to agricultural intensification. This study evaluates the effects of intensification level, habitat availability and rainfall on the population dynamics of this species. The population density of males was monitored for 7 years (2002–2008) at 184 points located within three sites with contrasting levels of agricultural intensification in southern Portugal. Densities decreased along the intensification gradient from 8.2 to 2.3 males / km2. Overall, there was an approximately 50% population decline during the period 2002–2008, driven by a decline observed in one of the less intensive sites, whereas in the other two sites densities remained fairly constant. Yearly variations in male densities were influenced by intensification level, amount of grassland habitat and rainfall patterns. Thus, agricultural intensification is having a negative effect on population densities of this threatened species, particularly through the loss of grasslands (fallow fields and pastures) suitable for displaying males. The results also suggest a positive impact of rainfall on male densities, although this is more likely in grasslands within less intensive agricultural regions of poorer soil quality, where higher breeding male densities occur. Grassland habitat quality, driven by both climate and human management, probably plays a major role in the population dynamics of this threatened steppe bird in its strongholds.