Efforts to protect tropical ecosystems aim at implementing biological corridors across the national territory of Costa Rica. However, potential near-future climate change challenges the effectiveness of such conservation measures. For this purpose, we developed near-future climate change scenarios at high spatial resolution using open-access global data from the Copernicus Climate Data Store (CDS). These projections resulted from downscaling (to a 1km2 national grid) and quantile-mapping bias-correction of the Essential Climate Variables Global Circulation Model (ECV_GCM) ensemble mean from the CDS using a moderate Representative Concentration Pathway 4.5 (RCP4.5). Projections were evaluated with limited local station data and applied to generate future ecosystem indicators (Holdridge Life Zones, HLZs). We show significantly increasing temperatures of 2.6°C with a spatial variability of ± 0.4°C for Costa Rica until 2040 with local differences (higher temperatures projected for the southern Costa Rican Caribbean). The future mean annual precipitation showed slightly wetter conditions (120 ± 43 mm/year) and most prominently in the Costa Rican Caribbean and south Pacific, but no significant drying in the north of Costa Rica by 2040. The bias-corrected climate data were aggregated to decadal and 30-year average (1971–2040) life zone ecosystem indicators that could potentially show ecosystem shifts. Changes in the life zones are most likely due to warmer temperatures and to a lesser extent caused by projected wetter conditions. Shifts are more likely to occur at higher elevations with a potential loss of the sub-tropical rainforest ecosystem. The projections support diminishing tropical dry forests and slightly increasing tropical rain and wet forests in the biological corridors of the driest and wettest regions, respectively. A countrywide spatial uniformity of dominating tropical moist forests (increase from 24% to 49%) at the expense of other HLZs was projected by 2040.