The energy transition requires the adoption of various hazardous chemicals to generate, transport and utilize energy. In this adoption process, value conflicts between stakeholders need to be considered to foster the social acceptance of these chemical molecules. To be able to anticipate on these value conflicts, this study aimed to develop and evaluate a methodological framework for analyzing and addressing value conflicts in the adoption of hazardous chemicals in the energy transition. By integrating principles from systems engineering and value-driven design methods, as well as input from experts in both fields, a framework was developed. The developed methodological framework consisted of three steps being: 1) Applying Systems Thinking to define the socio-technical system the chemical is adopted in and conceptualize stakeholder values (conceptual investigation), 2) Identifying values and value conflicts (empirical investigation) and 3) Classifying and addressing value conflicts (technical investigation). This approach innovates upon the default tripartite value-sensitive design approach by incorporating Systems Thinking in the conceptual investigation phase to suit the broader context of socio-technical systems design rather than just the design of physical technological artifacts like wind turbines and nuclear reactors. Furthermore, it combines parts of existing VSD frameworks in the empirical and technical investigation phase in a novel way. The methodological framework was evaluated by conducting a case study on the adoption process of ammonia in the Dutch energy transition. To inform the empirical investigation, 11 expert interviews with policy advisors, industry players and research experts provided in-depth information about the values and value conflicts at play. However, it was noted that the broad nature of the interview questions limited the ability to derive specific technical design requirements, suggesting that future studies should adapt the interview questions to focus on particular parts of the socio-technical system if desired. In the empirical investigation phase, value hierarchies were constructed from the value level to the norm level, which provided useful for identifying value conflicts. The results of the empirical investigation revealed seven major values which play a role in the adoption process of ammonia in the Dutch energy transition being: efficiency (of both spatial planning and the energy transition in general), competitiveness, cooperation, safety and health, environmental sustainability, transparency, and (procedural and distributive) justice. The values identified in this study were found to be comparable with those found in related works on the adoption of technologies like nuclear energy and wind turbines. Seven value conflicts were identified by comparing the norms related to each value and the framework was used to address and classify them. This allowed to derive policy implications. There is a need for more transparent communication with the public about the energy transition, available technology alternatives to reach net-zero, the associated risks of those alternatives, and the ethical dilemmas that the government is facing. It was established that local communities are willing to bear risks if the government clearly states what the ethical dilemmas are in the energy transition and the choices made in these dilemmas. This vision can build social acceptance from the industry and local communities and address the identified value conflicts between safety and health, justice, and efficiency. In this vision, the government should also address their standpoint on the ethical desirability of adopting certain chemicals in the energy transition. Therefore, it is necessary that the government has specified the intended use-cases for chemicals like green ammonia. This clarity can help address value conflicts related to competitiveness and environmental sustainability. Furthermore, it is important that the government keeps fostering a strong collaboration between industry and government. This is especially important when adopting chemicals that are new and where the government possesses limited expertise on. As the industry could possess the necessary technical expertise, the government could set regulatory boundaries upon collaboration with industry, enhancing regulatory preparedness. Moreover, to ensure that imported ammonia is produced green, certification standards should be put in place. These interventions could address the identified value conflict between environmental sustainability and competitiveness, fostering the social acceptance of ammonia adoption.