1. Throughout the tropics, regenerating secondary forests occupy vast areas previously cleared for agriculture and cattle ranching. However, despite the importance of regenerating forests in mitigating the pervasive negative consequences of forest loss and fragmentation on forest-associated biodiversity, longitudinal studies on species’ phylogenetic responses to matrix regeneration are rare.

2. We surveyed bats in continuous primary forest, primary forest fragments and in the regenerating secondary forest matrix of a whole-ecosystem Amazonian fragmentation experiment, ~15 and ~30 years after forest clearance, to investigate how changes in matrix quality through forest recovery affect phylogenetic α- and β-diversity.

3. We found that temporal changes in phylogenetic α-richness were more marked in the secondary forest matrix than in forest fragments and continuous forest, evidencing a significant increase in total evolutionary history over time. However, when the effects of species richness were accounted for, the phylogenetic structure of each assemblage was reduced close to zero, evincing a random pattern of lineages in all habitat types. Temporal differences in phylogenetic β-diversity were driven mainly by β_replacement in secondary forest and continuous forest ~30 years after forest clearance. Both habitats also clustered together in terms of β_richness, indicating similar levels of evolutionary heritage. Consequently, regenerating secondary forest showed a reduction in the extinction probability of lineages over time.

4. Synthesis and applications. Approximately 30 years of secondary forest regeneration were sufficient for phylogenetic richness to recover to levels similar to those observed in continuous forest. Promoting forest succession on degraded land through a combination of natural and active restoration, while ensuring the long-term protection of secondary forests regardless of their age is of key importance for conserving tropical bat diversity and their associated ecosystem services. Such restoration measures would stimulate the recolonization of fragments and matrix habitats by evolutionarily distinct bat species, safeguarding phylogenetically diverse assemblages and ecological functions. Our study suggests that forest restoration in tropical degraded areas should be encouraged and secondary forests be protected by law, especially in countryside ecosystems with high primary forest cover, and in the surroundings of protected areas.