The energy transition is a complex concept that requires progressively addressing various technical, environmental, social, and political issues. Green hydrogen is recognized as a clean fuel to support the energy transition worldwide. This study presents a modeling framework for green hydrogen deployment strategies in the transport and fertilizer sectors on a long-term basis. The mathematical model includes decision variables to account for the amount of hydrogen produced from different energy sources and the importation of fossil-based commodities. Additionally, it incorporates demand-supply and production capacity restrictions in 5-year intervals from the year 2020 to 2050. The case study focuses on the Ecuadorian context, and two deployment strategies are proposed: (i) utilizing surplus renewable energy and (ii) developing local PV capacity. Both strategies positively contributed to adopting more sustainable alternatives; however, Strategy II exhibited superior performance in terms of costs and GHG emissions. Thus, this work provides a framework for designing energy transition strategies and their evaluation to achieve specific renewable and green hydrogen adoption targets over time.