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Introduction: Two approaches were compared for the calculation of coefficient of variation (CV) and bias, and their effect on sigma calculation, when different allowable total error (TEa) values were used to determine the optimal method for Six Sigma quality management in the clinical laboratory. Materials and methods: Sigma metrics for routine clinical chemistry tests using three systems (Beckman AU5800, Roche C8000, Siemens Dimension) were determined in June 2017 in the laboratory of Peking Union Medical College Hospital. Imprecision (CV%) and bias (bias%) were calculated for ten routine clinical chemistry tests using a proficiency testing (PT)- or an internal quality control (IQC)-based approach. Allowable total error from the Clinical Laboratory Improvement Amendments of 1988 and the Chinese Ministry of Health Clinical Laboratory Center Industry Standard (WS/ T403-2012) were used with the formula: Sigma = (TEa − bias) / CV to calculate the Sigma metrics (σCLIA, σWS/T) for each assay for comparative analysis. Results: For the PT-based approach, eight assays on the Beckman AU5800 system, seven assays on the Roche C8000 system and six assays on the Siemens Dimension system showed σCLIA > 3. For the IQC-based approach, ten, nine and seven assays, respectively, showed σCLIA > 3. Some differences in σ were therefore observed between the two calculation methods and the different TEa values. Conclusions: Both methods of calculating σ can be used for Six Sigma quality management. In practice, laboratories should evaluate Sigma multiple times when optimizing a quality control schedule.