Cinnamon, clove, and lemongrass essential oils (EOs) and their active compounds cinnamaldehyde, eugenol, and citral, respectively, were investigated for their effectiveness as antimicrobial agents in an alginate-based edible coating (EC) on fresh-cut Fuji apples. This EC also contained malic acid, N-acetyl-L-cysteine, glutathione, and calcium lactate as quality stabilizing compounds. The EC applied on apple pieces effectively maintained the physicochemical characteristics of the apple pieces for more than 30 days, decreased the respiration rate, reduced the Escherichia coli O157:H7 population by about 1.23 log CFU/g at day 0, and extended the microbiological shelf life by at least 19 days. The addition of EOs at 0.7% (vol/vol) or their active compounds at 0.5% (vol/vol) into the EC increased its antimicrobial effect, reduced the E. coli O157:H7 population by more than 4 log CFU/g, and extended the microbiological shelf life by more than 30 days. However, those concentrations of EOs affected the physicochemical characteristics of fresh-cut apples and thus limited their shelf life from 7 to 21 days. Lemongrass and cinnamon EOs (0.7%), citral (0.5%), and cinnamaldehyde (0.5%) were the most effective compounds for extending microbiological shelf life, whereas lemongrass, cinnamon, and clove EOs at 0.3% (vol/vol) best maintained the physicochemical characteristics of the product. Apple pieces with EC at day 0 and with EC with or without lemongrass EO at 0.7% at day 15 were preferred by the panelists. ECs containing natural antimicrobials and quality stabilizing compounds may be useful for extending the shelf life of fresh-cut fruits.