Glucosylglycerol (GG) has a range of potential applications in health, pharmacy, and cosmetics due to its physiological, protein-stabilizing, and antioxidative properties. In addition to chemical synthesis and enzymatic catalysis, GG can be produced as a protective osmolyte in salt-stressed bacteria, such as the cyanobacterium Synechocystis sp. PCC 6803. Here, we presented an efficient GG production and secretion by genetically modified and encapsulated Synechocystis cells grown in a semicontinuous manner. We improved the production and secretion of GG in Synechocystis by first disrupting both the ggtC and ggtD genes, which encode the subunits of a GG uptake transporter, as well as the ggpR gene, which encodes a repressor for GG synthesis. Then, we confirmed that the rapid GG release from salt-stressed cells of Synechocystis depended on the ion gradient across the cell membrane. Finally, we proved the feasibility of an agar gel encapsulation method in supporting cell growth and the GG production of Synechocystis under semicontinuous culturing conditions.