The use of unconventional substrates (microalgae) associated with co-products (molasses) and exposure to magnetic fields (MF) may be a low-cost alternative to increase ethanol yield. This study aimed at evaluating the use of hydrolyzed biomass of Spirulina sp. with molasses as substrate for fermentation with Saccharomyces cerevisiae and MF application. It was evaluated the fermentation with culture medium composition 75% microalgal biomass and 25% molasses: 42 mT was applied throughout all the fermentation process (24 h). MF exposure affected positively just the ethanol consumption, increasing it by 1% when compared with no exposure. This result no reflected positively in the ethanol production, which reduced 8%. Yeast metabolism was influenced by MF application and the results indicate the complexity of MF actuation in the cell metabolism.