Due to its scarcity, researchers are synthesizing it through chemical, enzymatic, and microbial routes. Enzymatic methods are preferred to avoid unwanted impurities and harsh chemicals. However, large-scale production of rare sugars requires optimization of several parameters to increase yield and quality. A quick and efficient monitoring method is essential to optimize the enzymatic conversion process. Various analytical methods such as HPLC, GC-MS, LC-MS, NMR, SEC, and HPAEC-PAD are available for sugar analysis, but each has its limitations and may not be suitable for rare sugar analysis. Capillary electrophoresis (CE) has emerged as a promising technique for the separation and quantification of traditional sugars in food and plant materials. CE offers advantages like micro-volume samples, less reagent consumption, high resolution, sensitivity, and reproducibility, making it a potential tool for rare sugar analysis. The objective of this study is to develop a sensitive, simple, rapid, and cost-effective CE method for quantifying D-allose in the presence of five other sugars, including two more rare sugars (D-altrose and D-psicose). The method aims to overcome the limitations of existing analytical methods and provide accurate quantification and validation of D-allose during large-scale production from D-psicose in a continuous bioreactor. Through this investigation, we intend to establish a robust analytical method that enables efficient monitoring of D-allose production and facilitates the development of rare sugars as potential food additives or supplements for managing weight gain effectively.