Abstract Background This abstract outlines a comprehensive study on the application of Six Sigma methodologies to optimize internal quality control processes in a private biochemistry laboratory in India. Data collection was performed using Bio-Rad Assayed Chemistry Control on the Roche cobas 6000 instrument, facilitated by Bio-Rad Unity software. The study adheres to Clinical Laboratory Improvement Amendments (CLIA) 2024 guidelines, specifically focusing on Total Error (TEa). Methods The analytical performances of Cobas c501 insturment as analyse by running biochemical tests (urea, creatinine, uric acid, total bilirubin, AST, Amylase, Lipase, CK, LD, ALT, ALP, LDH, HDL-C, Ca2+, cholesterol, TG, HDL LDL, total protein, albumin, Na+, K+, and Cl−) and glucose on Cobas 400 were evaluated. Biases and CV were obtained from internal quality control programs using biorad unity software. The performance of each instrument was assessed using the σ scale; the benchmark performance was <3 σ (improvement needed); “world-class” quality was six sigma. Results Analytes such as “Alk PO4,” “ALT,” “Amylase,” “Bilirubin,” “CK,” “GGT,” “LD,” “Phosphorus,” “HDL,” “LDL Cholesterol,” “Triglycerides,” and “Uric acid” exhibited impressive sigma scores exceeding 6. Meanwhile, analytes including “Calcium,” “Total Cholesterol,” “Potassium,” “Total Protein,” “Urea,” and “Glucose” achieved sigma scores between 4 and 6, demonstrating noteworthy performance within acceptable bounds. Conclusions This study contributes valuable insights to laboratory management, specifically in the context of biochemistry testing in private Indian laboratories. The adoption of Six Sigma principles, coupled with adherence to CLIA 2024 guidelines and the utilization of advanced instrumentation and software, ensures compliance with regulatory requirements and fosters a culture of continuous improvement. This positions the laboratory to deliver high-quality and reliable results in the dynamic landscape of healthcare diagnostics.