A novel alcohol-free beverage with a fruity, slightly sour, sweetish, fresh, and plum-like flavor was produced by incorporating the edible mushroom shiitake (Lentinula edodes) into the fermentation process. Shiitake pellets were used as a biocatalyst to promote the synthesis of the fruity esters methyl 2-methylbutanoate and 2-phenylethanol from amino acids and an organic acid present in the wort. We investigated the impact of two critical process parameters (volumetric power input and inoculum concentration) on the morphology of, and flavor production by, the shiitake pellets in a 1 L stirred bioreactor. Increasing the volumetric power input and biomass concentration influenced the morphology of the pellets and promoted the production of the most important flavor compound methyl 2-methylbutanoate in the beverage. Furthermore the worty off-flavor methional was degraded during the cultivation in stirred bioreactor by shiitake pellets. These findings provide useful information to facilitate the scale-up of the biotransformation and fermentation process in bioreactors.