Instituto Juruá is an applied science organization, so most research has as a backdrop an important aspect for the conservation of biodiversity and traditional ways of life. One of Instituto Juruá's flagships is the development of a basin-scale conservation model for the entire Juruá River, integrating rural communities located in areas demarcated by Protected Areas, communities living outside these areas, and communities in indigenous lands. Among the topics covered, the following stand out:
* Impacts of Protected Areas on biodiversity and traditional ways of life.
* Impact of community management on biodiversity conservation and local well-being.
* Cascade effects of hunting-induced defaunation on forest regeneration.
* Models of environmental governance.
* Implementation status of Protected Areas.
* Collaborative management of natural resources.