•A comparative analysis is proposed with three territorial levels of study.•The compensation and potentiation works are formally punctual (Local level) and linear (Metropolitan and Cross-border regional level)•The referendum is a valid instrument for the construction of megaprojects.•Long-term articulated policies have an impact on empowering the Gotthard system.•Financing processes must be well structured with participatory mechanisms. The Gotthard transalpine base tunnel is located in Switzerland, it is considered the longest in the world. The purpose of this research is to detect the main effects of long-term policies on the occupation and transformation of cross-border land, in productive, industrial and commercial uses, due to the construction of the Saint Gotthard base tunnel, and the complementary works that enhance it. There are three levels of study proposed, three temporary scenarios (before, during and after the construction) and a comparative analysis with the future Lyon-Turin base tunnel. Maps are made with geodata from Switzerland, Italy and France and interviews with experts by class groups, this was essential to obtain a broader vision of the situation to be analyzed, it is concluded that the use of mixed methods proved to be useful for the stated objectives. A greater displacement of the impact at cross-border levels between Switzerland and Italy is demonstrated, with 43,776.6 ha of productive, industrial and commercial use, in relation to the cross-border areas between Italy and France of 15,593.6 ha related to the Lyon-Turin tunnel. Two types of compensation and empowerment works of the Gotthard System are identified and advantages in formulating long-term articulated policies and well-structured financing processes with participatory mechanisms. This research contributes to the current literature, aimed at researchers and policymakers on intermodal transport as a response to sustainable logistics.