New CO2 legislation forces the petroleum refining industry to review its operations and processes to cope with the new limitations of allowable CO2 emissions. Simultaneously, petroleum refineries, which are extremely complex entities, face another challenge represented by clean fuel products (low sulfur content) regulations. In an attempt to provide operational solutions to these issues, a CO2 management model was incorporated with an existing hydrogen management model that we have recently developed. To this end, this article presents an overall integrated model that solves simultaneously the refinery planning, hydrogen, and CO2 management problems. It addresses the optimum CO2 strategy selection through integration of refinery planning with the hydrogen network and CO2 emissions. The overall model was formulated as a mixed integer nonlinear program (MINLP). The model consists of the refinery emission sources and the considered mitigation options. Model performance was tested through different case studies with various reduction targets. The optimization results showed that the integration of the planning, hydrogen, and CO2 models lead to better profit margins and that CO2 mitigation options worked successfully together to meet a given reduction target. The obtained results also showed that the load shifting option can contribute up to a 3% reduction of CO2 emissions, while the fuel switching option can provide a 20% reduction. To achieve greater than 30% reductions, a CO2 capture technology must be employed in the petroleum refining industry.