In order to increase the typically low equilibrium CO2 conversion to methanol using commercially proven technology, the addition of two intermediate condensation units between reaction steps is evaluated in this work. Detailed process simulations with heat integration and techno-economic analyses of methanol synthesis from green H2 and captured CO2 are presented here, comparing the proposed process with condensation steps with the conventional approach. In the new process, a CO2 single-pass conversion of 53.9% was achieved, which is significantly higher than the conversion of the conventional process (28.5%) and its equilibrium conversion (30.4%). Consequently, the total recycle stream flow was halved, which reduced reactant losses in the purge stream and the compression work of the recycle streams, lowering operating costs by 4.8% (61.2 M€·a−1). In spite of the additional number of heat exchangers and flash drums related to the intermediate condensation units, the fixed investment costs of the improved process decreased by 22.7% (94.5 M€). This was a consequence of the increased reaction rates and lower recycle flows, reducing the required size of the main equipment. Therefore, intermediate condensation steps are beneficial for methanol synthesis from H2/CO2, significantly boosting CO2 single-pass conversion, which consequently reduces both the investment and operating costs.