Bacterial cellulose consisting of pure cellulose nanofibers, is a promising biomaterial with versatile applications. The primary producer is Komagataeibacter xylinus, however, its use is limited because the bacteria undergo irreversible conversion into a non-cellulose-producing mutant (Cel(-)) during shaking cultivation. Here, by investigating the bcs operon in Cel(-) mutants, we found that an IS element-inserted mutation in bcsA, is responsible for the conversion into Cel(-). To prevent IS element insertion into bcsA, putative IS element recognition sequences were modified. As a result, the engineered strain retained its own bcsA gene over seven sub-cultivations, and showed 1.7-fold higher productivity than wild-type strains without any differences of physical and chemical properties.