Ongoing tropical deforestation and forest degradation, combined with climate change, call for improved forest functional and biological diversity mapping to support increasingly tactical decision-making for conservation action. We combine a new map of forest canopy functional and biological composition with extensive protected area and indigenous land allocation data to quantify current protections and opportunities for new protections throughout the Peruvian Andes and Amazon region, a global biodiversity hotspot. The analysis is based on a map of 36 distinct Forest Functional Classes (FFC) covering >76millionha of forest at 1-ha spatial resolution. We find that while 42.6% of forests are under some form of protection, the percentage of protections applied to any particular FFC ranges from 20% to 69%. Under-represented FFCs are in the submontane and montane Andes, and in the northwestern Amazonian lowlands. Nationally-administered protections are uneven across the 36 FFCs, and regionally- and locally-administered protections are biased to relatively few mapped forest classes. Indigenous lands contain a relatively even distribution of FFC protections, providing the most FFC protection per unit forest area in Peru. Without the current portfolio of indigenous lands, the network of nationally-, regionally-, and locally-administered protected areas would greatly under-represent multiple functionally and biologically distinct FFCs throughout Peru. Mapping canopy functional diversity can support tactical approaches to protect a wider variety of forest types in a time of rapid environmental change.