The Andes of northern Peru are still widely covered with forests, but increasingly suffer from habitat fragmentation. Subsequent soil degradation often leads to the abandonment of overused forests and pastures. Ecological knowledge on the restoration potential, e.g., on dependencies of soil conditions and altitude, is scarce. Therefore, we compared soil and vegetation patterns along nine transects within the upper Pomacochas Basin, which is an important biodiversity corridor along the Andes, between remaining forests, succession sites and pastures. Anthropogenic successional and disturbance levels, geological substrate, and altitude have the most important ecological impacts on vegetation and tree species composition. Species responded to sandstone versus calcareous substrates, but also to depths of the organic soil layer, and light conditions. The absence of organic layers under pastures contrasted with the accumulation of thick organic layers under forest cover. Vegetation composition at succession sites revealed certain starting points (herbal stage, bush stage, or secondary forest) for restoration that will determine the length of regeneration paths. Pre-forest patches of Alchornea sp. and Parathesis sp. may act as habitat stepping stones for expeditiously restoring biocorridors for wildlife. The key findings can contribute to the sustainable use and conservation of biodiversity in a fragile ecoregion.