Capillary electrophoresis sodium dodecyl sulfate (CE-SDS) has become a popular technique for protein purity analysis in biopharmaceutical laboratories due to its high resolution, reproducibility, automation ability and quantitative protein separation capability. Here, we present a multi-capillary electrophoresis system, the BioPhase 8800 system, that is robust, reproducible and capable of multiplexing CE-SDS analysis of AAV capsid proteins. The study that is discussed demonstrates that the platform can perform 8 separations in parallel with significantly improved throughput. In the study, a multi-capillary electrophoresis system was used to accelerate sample preparation method optimization for AAV capsid purity analysis. The sample buffer concentration, the SDS percentage and the incubation temperature for the AAV sample preparation were optimized. Analysis using the multi-capillary system allowed for a 12x faster analysis time compared to using the single-capillary PA 800 Plus system. Optimized conditions obtained on the multi-capillary system correlated well with the values obtained on the PA  800 Plus system, providing a seamless and easy method transfer from the single- to the multi-capillary platform. The BioPhase 8800 system is equipped with both ultraviolet (UV) and laser-induced fluorescence (LIF) detection options. For better sensitivity, samples were labeled with Chromeo dye for LIF analysis. The labeling was simple and did not require any buffer exchange for sample cleanup. This helped decrease sample preparation time and overall workflow completion time. Analysis of 3 different AAV serotypes (AAV1, AAV2 and AAV8, respectively) was performed on both the PA 800 Plus system and the BioPhase 8800 system.