Andean tropical montane forests (TMF) are hotspots of biodiversity that provide fundamental hydrological services as well as carbon sequestration and storage. Agroforestry systems occupy large areas in the Andes but climatic pressures, market volatility and diseases may result inagroforest abandonment, promoting secondary succession. Secondary forests are well-adapted and efficient carbon sinks whose conservation is vital to mitigate and adapt to climate change and to support biodiversity. Little is known, however, about how secondary TMF recover their aboveground biomass (AGB) and composition after abandonment. We established a 1.5 ha plot at 1780 masl on a 30-year old abandoned agroforest and compared it against two control forest plots at similar elevations. Agroforestry legacies influenced AGB leading to far lower stocks (42.3 ± 5.4–59.6 ± 7.9 Mg ha−1 using allometric equations) than those expected after 30 years (106 ± 33 Mg ha−1) based on IPCC standard growth rates for secondary montane forests. This suggests a regional overestimation of mitigation potentials when using IPCC standards. Satellite-derived AGB largely overestimated our plot values (179 ± 27.3 Mg ha−1). Secondary growth rates (1.41–2.0 Mg ha−1 yr−1 for DBH ≥ 10 cm) indicate recovery times of ca. 69 to 97 years to reach average control AGB values (137 ± 12.3 Mg ha−1). This is 26 years above the average residence time of montane forests at our elevation (71 ± 1.91 years) suggesting a non-recovery or far slower recovery to control AGB values. Three variables appear to define this outcome compared to the control plots: lower DBH (15.8 ± 5.9 cm vs 19.8 ± 11.0 cm), lower basal area (12.67 ± 0.7 vs 28.03 ± 1.5 m2 ha−1) and higher abundance of lighter-wood tree genera (0.46 ± 0.10 vs 0.57 ± 0.11 gr cm3) such as Inga, a common shade-tree in Andean agroforests. With 3.2 million hectares committed to restoration, Peru needs to target currently neglected TMF recovery schemes to support biodiversity, water and carbon storage and fulfill its international commitments.