AbstractQuestionsMost rivers in theWesternCapeProvince ofSouthAfrica are heavily invaded by alien trees, often resulting in profound changes in biodiversity and ecosystem functioning. Although large‐scale management operations are underway to clear invasive trees and restore ecosystem function, little is known regarding native species recovery after alien clearing. HasEucalyptusinvasion along theBergRiver altered the distribution and composition of native vegetation? How does the removal of invasive trees through complete clearing and thinning facilitate the recovery of native vegetation?LocationBergRiver,WesternCape,SouthAfrica.MethodsWe assessed the recovery of native vegetation after 4 yr of complete clearing of the invasive treeEucalyptus camaldulensis(100% alien cover removal) and thinning (40–50% alien cover removal) along theBergRiver in theWesternCape,SouthAfrica. Native and alien plant cover, species richness and diversity were recorded on completely cleared and thinned sites and compared to natural (non‐invaded control sites) andE. camaldulensisinvaded sites.ResultsSpecies richness and diversity were significantly higher in both completely cleared and thinned sites compared to natural and invaded sites. Increases in species richness and diversity in completely cleared and thinned sites were a result of re‐invasion by alien herbaceous and graminoid species, which have the potential to hinder native species recovery. Cover of native trees and shrubs was higher in both completely cleared and thinned sites compared to invaded sites. Species composition (relative cover) in completely cleared and thinned sites was similar to species composition in natural sites.ConclusionsBoth complete clearing and thinning methods promote indigenous vegetation recovery and a positive trajectory towards recovery of ecosystem structure and composition can be expected in future. To improve management operations, a four‐stage thinning process that has the potential to facilitate native species recovery is suggested.