The production of fossil fuels to satisfy the energy demand has caused a drastic increment in the greenhouse gas emissions, which are associated directly with the global warming problem. Installing biorefineries is an interesting alternative to address this problem because biomass can capture CO2 emissions during its growth. On the other hand, a new interesting approach to promote economic growth in low-income regions is through new eco-industries dedicated to cultivate trees and taking care of the forest. These forest plantations help to capture CO2 emissions produced by petroleum refineries and biorefineries. Therefore, a system able to integrate production of fuels through refineries and biorefineries with the use of forest plantations to decrease the greenhouse gas emissions can be an attractive solution to significantly improve the environmental sustainability. However, the implementation of this project has to consider several factors, including the life time of the project, the availability of resources, the amount and type of products that should be produced, the allocation and capacity of the involved refineries, biorefineries and forest plantations, among others. For this reason, this paper presents an optimization model for the optimal planning of an integrated system for the production of fossil fuels and biofuels considering the interaction with eco-industries, which are able to capture emissions from biorefineries and refineries and receive an economic benefit. The proposed mathematical model takes into account the availability of biomass, the production of oil, a set of existing biorefineries and refineries as well as the possibility to install new facilities. The mathematical approach was applied to a nationwide case study from Mexico, considering the creation of new jobs, overall emissions and net profit as objectives. The results are shown through a Pareto curve, which is useful to make decisions about the planning of the interactions between these types of industries as well as determining the supply chain configuration in order to satisfy overall demand of products.