Balearic Islands are facing challenges related to energy demand and reliance on imported fossil fuels. In this context, hydrogen vector could be part of the technical solutions for increasing the contribution of renewable energies towards various energy demand sectors. This paper explored the use of dynamic simulation and optimization as a mean for assessing the achievable economic and environmental performance of hydrogen pathways under the specific fluctuating boundary conditions of these Islands. A bi-objective dynamic optimization approach based on a Mixed Integer Linear Programming approach has been implemented using PERSEE software to assess the tradeoffs between costs and carbon emissions of hydrogen supply chains. The chosen case study has been built using some of the technical features of the European GreenHysland project located in Balearic Islands. The optimization of the design and operating conditions of hydrogen chains involving two modes of hydrogen transport (trucks and pipeline) has been addressed, for the supply of hydrogen to fuel cell buses and taking into account the possibility of injecting hydrogen into the natural gas network. The economic and environmental optimizations resulted in different electrolyzer’s operation strategies. On one hand the economic optimization led to high use rate of the electrolyzer (92 %) and high carbon impact of hydrogen due to high carbon content of grid electricity. On the other hand the environmental optimization led to a PV-following strategy with a low use rate of the electrolyzer (50 %). It was shown that in current situation, due to the high greenhouse gases intensity of Balearic electrical grid, the conditions for hydrogen to provide a net carbon advantage compared with fossil reference scenario would be to ensure a minimal direct PV share of 40 % in the electricity consumed by the electrolyzer, thus resulting in a running time availability lower than 63 % and an average use rate lower than 75 % of nominal capacity. From a greenhouse gas perspective, it was shown that the best choice would be to encourage direct solar electricity sourcing for the electrolyzer as well as maximizing injection into the natural gas grid. Finally, results showed that the choice of truck or pipeline for hydrogen transport does not have a significant influence on the total emissions compared to the influence of operation strategy. This study confirmed the interest of the dynamic optimization approach combined with epsilon-constraint method for the design of hydrogen projects to comply with future certification requirements for green or low-carbon hydrogen. In future work, the comparison of hydrogen systems with alternative energy supply chains should be extended to other categories of environmental impact through multi-objective optimization methods. Finally, innovative modeling and optimization methods should be developed to evaluate different hydrogen deployment strategies and infrastructure planning in the Balearic Islands’ future energy landscape.