Lactobacillus fermentum is commonly responsible for fruit juice fermentation and spoilage. The aim of this study was to investigate the potential use of nerolidol to control the spoilage of fresh orange juice by L. fermentum. Nerolidol was incorporated into hydroxypropyl-β-cyclodextrin inclusion complex, conventional liposome, and drug-in-cyclodextrin-in liposome systems. The systems were lyophilized and characterized with respect to their nerolidol content, size, and morphology. The effects of the acidity and cold storage of orange juice on the survival of L. fermentum were evaluated. Subsequently, the antibacterial activity of nerolidol in refrigerated orange juice was assessed at pH 3.3. Nerolidol showed a faster antibacterial activity at 4 000 μM (5 days) compared to 2 000 μM (8 days). Under the same conditions, the inclusion complex completely killed bacteria within 6 days of incubation at 4 000 μM, suggesting its potential application in fruit juices. Nerolidol-loaded liposomes did not exhibit an antibacterial activity and altered the appearance of juice.