European islands have been leading the charge in renewable energy innovation. Yet, the intermittent nature of sources like solar and wind poses challenges such as grid saturation and frequency variations. Limited interconnection with mainland grids exacerbates these issues, necessitating backup from conventional power sources during low-production periods. Until 2021, Crete operated independently, but new infrastructure now integrates it with the Greek mainland grid, facilitating swift energy transfers. This integration enables surplus power from Crete’s solar and wind systems to be transmitted to the mainland and vice versa. However, reliance on remote power production exposes the island to market fluctuations and distant disruptions, impacting electricity production. Storage technologies offer a solution, enhancing renewable energy penetration while reducing carbon emissions. Green hydrogen, a rising storage method, shows promise in offsetting carbon emissions. Its clean-burning nature minimizes environmental impact and reduces reliance on costly and harmful conventional sources. This study aims to evaluate the feasibility of achieving carbon-neutral electricity production in Crete, Greece, using hydrogen storage to offset annual carbon emissions in a financially viable and sustainable manner. Hydrogen’s clean-burning properties reduce environmental impact and lessen dependence on expensive and environmentally harmful conventional sources. The methodology prioritizes the independence of the Cretan electricity system, utilizing electrolysis to produce green hydrogen and proton-exchange membrane (PEM) fuel cells for energy generation. It investigates the optimal expansion of renewable energy systems, including photovoltaic (PV) and wind turbine (WT) parks, alongside the installation of hydrogen storage, under specific assumptions. This proposed installation aims to achieve both island independence and profitability, requiring an additional expansion in PV capacity of 2.13 GW, WT capacity of 3.55 GW, and a hydrogen system with electrolyzer and fuel cell capacities totaling 278.83 MW each, along with a hydrogen tank capacity of 69.20 MWh. The investment entails a capital expenditure (CAPEX) of 6,516,043,003.31 EUR for a nearly zero net present value (NPV) over 20 years. However, carbon neutrality cannot be attained through this optimal solution alone, as relying solely on carbon sequestration from olive groves, the primary crop cultivated on the island, is insufficient as a carbon sink method. The annual net carbon emissions from electricity production, island transport, residential heating, and carbon sequestration are estimated at 94,772.22 tCO2.