Few studies describe the factors that influence the natural regeneration in abandoned gold mining areas in the Amazon. Here we focus on the influence of the distance to the forest edge and abandonment time in a spontaneous succession of degraded areas by gold mining in the southeastern Peruvian Amazon. We assessed woody species composition (DBH ≥ 1 cm) and forest stand structure across a chronosequence (2–23 years). A total of 79 species belonging to 30 families were identified. The natural regeneration was dominated by Fabaceae, Malvaceae, and Urticaceae. Together, they represented 60% of the importance index. Cecropia membranacea and Ochroma pyramidale were the dominant pioneer species at the initial successional stage. The basal area and species diversity were directly related to time after abandonment and inversely related to the distance to forest edges. The distance-based redundancy analysis showed that more of the variation in species composition was explained by distance to the forest edge than the abandonment time. Our study revealed that regeneration was relatively slow and provided evidence that the distance to the forest edge is important for natural regeneration in areas degraded by gold mining.