Understanding the factors limiting population growth is crucial for species management and conservation. We assessed the effects of seed and microsite limitation, along with climate variables, on Helianthemum squamatum, a gypsum soil specialist, in two sites in central Spain. We evaluated the effects of experimental seed addition and soil crust disturbance on H. squamatum vital rates (survival, growth and reproduction) across four years. We used this information to build integral projection models (IPMs) for each combination of management (seed addition or soil disturbance), site and year. We examined differences in population growth rate (lambda) due to management using life table response experiments. Soil crust disturbance increased survival of mid to large size individuals and germination. Contributions to lambda of positive individual growth (progression) and negative individual growth (retrogression) due to managements varied among years and sites. Soil crust disturbance increased lambda in the site with the highest plant density, and seed addition had a moderate positive effect on lambda in the site with lowest plant density. Population growth rate (lambda) decreased by half in the driest year. Differences in management effects between sites may represent a shift from seed to microsite limitation at increasing densities. This shift underscores the importance of considering what factors limit population growth when selecting a management strategy.