Colombia is a notorious biodiversity hotspot that came to the spotlight of conservation upon the signing of the peace agreement in 2016. Here we used a counterfactual approach to forecast by 2036 the impact of deforestation on Colombia’s biodiversity and carbon stocks under three scenarios: (1) pre-signing of the peace agreement, (2) post-signing and (3) business-as-usual. We found that if deforestation rates continued at the same pace of post-signing, up to 41,000 km2 of forest area may be lost by 2036, whereas pre-signing rates would save nearly 25,000 km2 (equivalent to the total forest loss observed between 2000 and 2018). Under the pre-signing scenario, between 2018-2036 Colombia would reduce the average impact on the range of forest-specific species by nearly 50% of habitat area relative to 2000-2018, whereas under the post-signing scenario, it would increase by 33%. Moreover, losses of 312-807 Mm3 of growing stock volume and 267-688 Mt of aboveground biomass were projected by 2036, jeopardizing the country’s commitments towards international conservation as well as climate targets. Importantly, we found a mismatch at the department level on biodiversity and biomass losses, which highlight an urgent need to generate coherent policies at a national level aiming to tackle both issues.