The olive oil production sector faces many problems in terms of plants’ operation, while several environmental problems are also encountered, including the cultivation, harvesting of olives and standardization processes. Furthermore, it has been estimated that the percentages of energy consumption during olive oil production far exceed the permissible limits, thus presenting a negative environmental footprint. During recent years, a lot of effort has been put to overcome these issues, providing approaches for the proper management of process residues and energy saving in production plants. The project presented here aims at optimizing the process of virgin olive oil production by adopting feasible practices that treat with the olive oil production, as a whole. Furthermore, principles of the Circular Economy are implemented for residues treatment to decrease the pollution of the soil, water and air. An advanced model for calculating mass and energy balances (inflows-outflows) at every stage of the process has been also developed, to provide the necessary energy for the off-grid operation of the unit. Regarding the standardization process, we also propose alternatives to reduce excessive energy consumption and utilize the remnants of the process. Finally, the sensitivity of our models on the parameters’ values has been examined, as well. The application of the above methods corresponds to an optimized olive-oil production, presenting significant reduction of energy wastes (more than 20%). In conclusion, it has been proved here that the proposed model of rural development in the oil industry is sustainable, effective in controlling the quality of virgin olive oil and presents a positive environmental footprint.