Owing to its important nutritional features, extra virgin olive oil (EVOO) is one of the world’s highest-value products, mostly manufactured in Mediterranean countries. However, its production exerts several negative environmental effects, mainly related to the agricultural phase (and the use of fertilizers, pesticides, etc.) and waste management. Olive oil can be extracted from the olive paste using different extraction systems, including pressure, centrifugation, and percolation. In particular, EVOO by-product composition strictly depends on the extraction technologies, and two- or three-phase centrifugal extraction methods are usually employed. Therefore, due to olive oil’s economic value, it might be useful to investigate its environmental impacts, to advise sustainable supply chain models. In this context, a valuable tool for assessing the product’s environmental compatibility is the Life Cycle Assessment, which is part of a broader Life Cycle Thinking philosophy. This research focused on evaluating the EVOO environmental impact by comparing two- and three-phases extraction processes. Additionally, two scenarios, (i.e., composting and bio-gasification), were proposed to assess the best valorisation strategy for the produced pomace. The results showed that the two-step extraction process was more sustainable than the three-step one in nine out of nine considered impact categories. By milling 1000 kg of olives, the first technology approximately produces 212 kg CO2 eq, the latter 396 kg CO2 eq. Finally, pomace valorisation by bio-gasification was found as the best recovery process, able to confer greater environmental benefit than composting.