Successful restoration measures need a good understanding of how the composition, structure, and functioning of ecosystems change with degradation and what the best indicators of these changes are. To answer these questions, we worked on four ecosystem types in the Mediterranean Andes mountains in central Chile (from sclerophyllous forest to Andean shrublands), which represent an elevational gradient from 700 to 3,250 m. We sampled three plots on each of the three degradation levels (low, medium, and high) for each ecosystem at increasing distances from goat corrals. We measured 35 indicators that describe vegetation (14), soil (15), and ecosystem processes (6) for one growing season. Degradation caused a decrease in shrub cover, shrub productivity, the Normalized Community Structure Integrity Index (CSIIn), litter depth, total soil nitrogen and C/N ratio, and an increase in clay content. Plant species indicating low degradation were consistently native woody species. When comparing ecosystems (i.e., at different elevations) against the type of variable, process-based indicators showed more statistically significant differences. Based on their consistency across ecosystems and ease of measurement, we recommend using shrub cover and litter depth as indicators of degradation. Finally, we concluded that ecosystems are highly degraded when vegetation- and process-based indicators change ∼ 60% or when soil indicators change ∼ 25%. These results could also be used to set goals for restoration projects in these mountain ecosystems.