Aldonic acids are receiving increased interest due to their applications in nanotechnology, food, pharmaceutical and chemical industries. Microbes with aldose-oxidizing activity, rather than purified enzymes, are used for commercial production with limited success. Thus it is still very important to develop new processes using strains with more efficient and novel biocatalytic activities for the production of adonic acids. In the present study, Pseudomonas fragi TCCC11892 was found to be an efficient producer of aldonic acids, with the production of galactonic and L-rhamnonic acid by P. fragi reported for the first time. The semi-continuous production of maltobionic acid and lactobionic acid was developed for P. fragi TCCC11892, achieving a yield of over 90 g L⁻¹ for the first 7 cycles. The excellent performance of P. fragi in the production of lactobionic acid (119 g L⁻¹) was also observed when using waste cheese whey as an inexpensive fermentation medium. Scaling up of the above process for production of aldonic acids with P. fragi TCCC11892 cells should facilitate their commercial applications.