The effects and consequences of global warming on the productivity of the Patagonian forest are still unknown. The use of Unmanned Aerial Vehicles (UAV) promotes new knowledge of the most pristine and unknown sub-antarctic forests located in Chilean Patagonia. This work presents an initial approach to spatialize biochemicals over the Patagonian forests using ultra-high spatial resolution imagery acquired from UAVs equipped with a multispectral (visible, near-infrared, and thermal) sensor. The images were obtained in multiple flights over the Cerro Castillo National Park (Aysén Region, Chile), and several Vegetation Indices (VIs) were estimated. Leaves of Nothofagus pumilio (Poepp. et Endl.) Krasser (Nothofagaceae) individuals were extracted after the flights and were then used to determine the biochemicals traits of chlorophylls (Chl-a and Chl-b) and carotenoids pigments, as well as the total phenolic content (TPC), total flavonoids content (TFC), and the DPPH radical scavenging assay. Their relationships with multiple VIs was analyzed in order to assess the spatiality of the biochemicals traits in the forest during it most productive phenological stage. Results showed high correlations for the biochemical traits pigments (R2 > 0.75) with the indices DVI, MCARI, and MSAVI1 as the best performing indices, while further spectral availability is needed for significant correlations with biochemicals traits related to the antioxidant capacity. Spatialization of the biochemical traits within UAV imagery was also performed evaluating their representation in the forest. This work allowed us to identify the different spectral behavior of the N. pumilio species, its relation to biochemical traits, and their spatialization, thus presenting the first step to developing a monitoring protocol for the evaluation of the Patagonian forests under the current global warming scenarios in the region.