The aim of this research was to extend an existing capillary electrophoresis (CE) method, originally developed for the determination of mono- and disaccharides, to the determination of alternative carbohydrate compounds, namely furfural and polydatin. Empirical validation confirms that this novel method can be applied for the determination of analyte concentrations from complex matrices, and the evaluation of their carbohydrate composition. It is concluded that the approach has validity as an analytical procedure and has the ability to determine industrially important analytes from a heterogeneous biological sample matrix, and thus, the method adds value to the development of large scale separation processes. However, some additional optimization is required before online applications.