The fruit of Schisandra chinensis, Omija, is a well-known traditional medicine used as an anti-tussive and anti-diarrhea agent, with various biological activities derived from the dibenzocyclooctadiene-type lignans. A high-pressure liquid chromatography-diode array detector (HPLC-DAD) method was used to determine seven lignans (schisandrol A and B, tigloylgomisin H, angeloylgomisin H, schisandrin A, B, and C) in the different plant parts and beverages of the fruit of S. chinensis grown in Korea. The contents of these lignans in the plant parts descended in the following order: seeds, flowers, leaves, pulp, and stems. The total lignan content in Omija beverages fermented with white sugar for 12 months increased by 2.6-fold. Omija was fermented for 12 months with white sugar, brown sugar, and oligosaccharide/white sugar (1:1, w/w). The total lignan content in Omija fermented with oligosaccharide/white sugar was approximately 1.2- and 1.7-fold higher than those fermented with white sugar and brown sugar, respectively. A drink prepared by immersion of the fruit in alcohol had a higher total lignan content than these fermented beverages. This is the first report documenting the quantitative changes in dibenzocyclooctadiene-type lignans over a fermentation period and the effects of the fermentable sugars on this eco-friendly fermentation process.