Data collection from large areas of native forests poses a challenge. The present study aims at assessing the use of UAV for forest inventory on native forests in Southern Chile, and seeks to retrieve both stand and tree level attributes from forest canopy data. Data were collected from 14 plots (45 × 45 m) established at four locations representing unmanaged Chilean temperate forests: seven plots on secondary forests and seven plots on old-growth forests, including a total of 17 different native species. The imagery was captured using a fixed-wing airframe equipped with a regular RGB camera. We used the structure from motion and digital aerial photogrammetry techniques for data processing and combined machine learning methods based on boosted regression trees and mixed models. In total, 2136 trees were measured on the ground, from which 858 trees were visualized from the UAV imagery of the canopy, ranging from 26% to 88% of the measured trees in the field (mean = 45.7%, SD = 17.3), which represented between 70.6% and 96% of the total basal area of the plots (mean = 80.28%, SD = 7.7). Individual-tree diameter models based on remote sensing data were constructed with R2 = 0.85 and R2 = 0.66 based on BRT and mixed models, respectively. We found a strong relationship between canopy and ground data; however, we suggest that the best alternative was combining the use of both field-based and remotely sensed methods to achieve high accuracy estimations, particularly in complex structure forests (e.g., old-growth forests). Field inventories and UAV surveys provide accurate information at local scales and allow validation of large-scale applications of satellite imagery. Finally, in the future, increasing the accuracy of aerial surveys and monitoring is necessary to advance the development of local and regional allometric crown and DBH equations at the species level.