Ecuador will experience a significant expansion of the oil industry in its Amazonian region, one of the most biodiverse areas of the world. In view of the changes that are about to come, we explore the conflicts between oil extraction interests and biodiversity protection and apply systematic conservation planning to identify priority areas that should be protected in different oil exploitation scenarios. First, we quantified the current extent of oil blocks and protected zones and their overlap with two biodiversity indicators: 25 ecosystems and 745 species (whose distributions were estimated via species distribution models). With the new scheme of oil exploitation, oil blocks cover 68% (68,196 km2) of the Ecuadorian Amazon; half of it occupied by new blocks open for bids in the southern Amazon. This region is especially vulnerable to biodiversity losses, because peaks of species diversity, 19 ecosystems, and a third of its protected zones coincide spatially with oil blocks. Under these circumstances, we used Marxan software to identify priority areas for conservation outside oil blocks, but their coverage was insufficient to completely represent biodiversity. Instead, priority areas that include southern oil blocks provide a higher representation of biodiversity indicators. Therefore, preserving the southern Amazon becomes essential to improve the protection of Amazonian biodiversity in Ecuador, and avoiding oil exploitation in these areas (33% of the extent of southern oil blocks) should be considered a conservation alternative. Also, it is highly recommended to improve current oil exploitation technology to reduce environmental impacts in the region, especially within five oil blocks that we identified as most valuable for the conservation of biodiversity. The application of these and other recommendations depends heavily on the Ecuadorian government, which needs to find a better balance between the use of the Amazon resources and biodiversity conservation.