The project would violate the Collective Rights of the Pueblo Montubio, indigenous communities located along the coast of the nearby the project site. The community of Río Manta has filed two complaints about the project in the Constitutional Court, on the grounds that a) project did not respect a petition regarding communities' collective territory and paid indemnification of the purchased territory from previous owner of the property, La Fabril, and b) the project sponsors did not conduct FPIC procedures in assessing the impact of the refinery on communities.

Ecuadorean NGOs, incuding Ecuadorean human rights group Center for Economic and Social Rights and environmental coalition Leave It In the Ground, strongly suspect that oil for the refinery may be supplied from the Yasuní National Park. Yasuní National Park is considered to be one of the most biodiverse regions in the world and was named a biosphere region by UNESCO. The region is home to numerous indigenous peoples, with some living in voluntary isolation. Oil drilling would essentially dispossess indigenous communities of their livelihood and culture. Additionally, extractive activities on the lands of indigenous peoples in voluntary isolation is classified as "ethnocide" in article 57 of the Ecuadorian constitution. Numerous communities, including those from the Shuar, Kitchwa, Waorani communities and the Tagaeri and Taromenane clans, would be irreparably impacted. In 2014, more than 700,000 signatures were collected to urge President Rafael Correa to conduct a public consultation on keeping Yasuní oil in the ground. However, Correa denied the request. Since then, Yasuní has become the most contentious issue between Ecuador's environmental movement and its government.