Biodiversity loss is a growing concern globally, but there’s a lack of knowledge on where to focus conservation efforts. It is therefore essential to determine priorities and barriers to biodiversity knowledge generation. In this context, we present evidence from the Philippines on how sociopolitical instability drives biodiversity shortfall. Our study showed that conflict leads to fewer biodiversity records, with low-conflict areas having higher turnover by more than 50%. Further, tree cover loss is lower in high-conflict areas. Security risks due to sociopolitical conflicts can significantly affect biodiversity recording efforts, potentially leading to underestimating species diversity in these regions. This study highlights the link between conflicts and biodiversity shortfalls, and the negative impact on biodiversity documentation efforts. While rare positive consequences exist, they are incidental and overall negative. Addressing the convergence of conflict, extremism, and biodiversity conservation is crucial for safeguarding ecosystems and human and nature's well-being.