The Galapagos Islands have a protected marine reserve that currently gets most of its energy—over 80%—from fossil fuels like diesel. This reliance on fossil fuels is a significant issue because it impacts the environment and sustainability of the region. Understanding this heavy dependence is important for exploring alternatives that can provide cleaner energy. This paper introduces a new simulation model based on system dynamics to explore the effects of completely replacing fossil fuels with biodiesel as a short-term solution. The simulation uses current official data for the Galapagos Islands and connects different factors to calculate their effects all at once. Our goal is to identify the social, economic, energy-related, and environmental factors that make biodiesel a better choice than the currently used fossil fuels. We aim to find a way to keep the energy supply stable, as it mainly depends on internal combustion engines, while also quickly providing cleaner and greener energy with the resources we already have. Biodiesel can completely replace fossil fuels as an immediate short-term solution in the Galapagos Islands, providing a viable and advantageous option for energy supply that optimizes economic, social, energetic, and environmental conditions. With an adoption rate of 0.003—meaning that 3 out of every 1,000 people who currently use diesel switch to biodiesel each year—it is possible to establish biodiesel as the main fuel over a period of 5 years. In addition to using biodiesel as the only fuel source, within 5 years, it could cost 31.7% less if locally produced compared to diesel based on international prices. By 2050, CO2 emissions could drop from 8 million tons to 1 million tons. Our simulation, using real data, shows that adopting biodiesel within the current infrastructure is both viable and beneficial. It optimizes economic, social, energy-related, and environmental factors. We recommend this approach before adopting new technologies that claim zero CO2 emissions, as their potential environmental impacts are still unknown.