In the Peruvian highlands, climate change and inadequate management are causing land degradation and collapse of the pastoral system. Our research project was aimed at assessing the impact of grazing on dry Puna ecosystem, as understanding and predicting vegetation changes in harsh environments in the face of different disturbance regimes is required for aware and effective management. The study area was the Salinas and Aguada Blanca National Reserve. Two experimental areas were selected, characterized by deep soils with gentle slopes and by shallow soils with steeper slopes. In each area, sites with low and high disturbance regimes were identified, and vegetation was sampled using 10 × 10 m plots. The results indicated that the environmental constraints have a marked influence on the species composition, while disturbance quantitatively affects diversity. The floristic changes observed under different disturbance intensities are mainly related to the functional differentiation of the plant communities and to the decrease in vegetation cover. These processes pose a serious risk to the livelihood of the local people, because they can lead to the loss of biodiversity and economic value of pastures, as well as to soil erosion.