The functionalization methods of materials based on bacterial cellulose (BC) mainly focus on the chemical modification or physical coating of fermentation products, which may cause several problems, such as environment pollution, low reaction efficiency and easy loss of functional moieties during application. Here, we develop a modification method utilizing the in situ microbial fermentation method combined with 6-carboxyfluorescein-modified glucose (6CF-Glc) as a substrate using Komagataeibacter sucrofermentans to produce functional BC with a nonnatural characteristic fluorescence. Our results indicate that the microbial synthesis method is more efficient, controllable and environmentally friendly than traditional modification methods. Therefore, this work confirms that BC can be functionalized by using a microbial synthesis system with functionalized glucose, which provides insights not only for the functionalization of BC but also for the in situ synthesis of other functional materials through microbial synthetic systems.