Abstract Background External quality assessment (EQA) is essential for evaluating the performance of clinical laboratories and improving the quality of their analytical procedures. The Mongolian External Quality Assessment Scheme (MEQAS) has been established by organizations under the Ministry of Health to fulfill this purpose. The aim of this study is to provide a comprehensive summary of the inter-laboratory variation in biochemistry parameters among laboratories in Mongolia over a twelve-year period. Methods Three types of control materials were utilized: QAP-Trol Normal and Pathological levels, manufactured by Sysmex, and Pooled serum, prepared by combining leftover serum of patients. Samples were distributed semi-annually to laboratories, with participants measuring them promptly within three days. Results for 23 biochemistry parameters were submitted within a week via the “SmartEqas” software, enabling for analysis based on method and analyzer, and calculating standard deviation index (SDI), coefficient of variation (CV), and bias percentage (Bias%). Results In comparing the initial and most recent surveys, the number of participants has increased by nearly four times, rising from 55 to 217. Notably, the proportion of fully automatic users surged from 23.6% to 86.6%, a trend attributed to the establishment of numerous new laboratories and a growing recognition of the importance of EQA. Changes in the inter-laboratory coefficient of variation (CV) for each parameter were assessed from the initial to the recent period by calculating the mean of changes. In the recent assessments, CVs decreased to less than 10% for 14 parameters, including AST, ALT, UN, CRE, GLU, and others. Certain parameters, such as K, GLU, and Urea, exhibited markedly reduced variation from 16.3%, 12.1%, and 22.2% to 2.9%, 7.4%, and 9.3%, respectively. Conversely, some parameters, including LD (L-P), GGT, AMY (1), ALP (2), UA, TBIL, DBIL, FE, and MG, displayed gradual reductions in CVs to 10-20% compared to the initial period. In contrast, the coefficient of variation (CV) for four parameters: LD (P-L), AMY (2), ALP (3), and ALP (4), has not shown significant decreases and remains high, exceeding 20%. Conclusions Despite participation not being mandatory, laboratories in Mongolia exhibit a strong willingness to engage in the assessment process. The implementation of MEQAS has yielded tangible benefits, a reduction in inter-laboratory variation for most biochemistry parameters, with some achieving international level. While this improvement can be attributed to the streamlining of measurement methods, similar to outcomes observed in other countries, it is important to acknowledge the persistence of random and systematic errors. However, it is worth noting that certain parameters still exhibit higher CVs compared to similar studies. This discrepancy may be attributed to the inherent variation in enzymes among different methods and manufacturers. Hence, there is a clear need for continuous improvement measures and knowledge-sharing initiatives with other nations to address these challenges. Evaluating and implementing such measures at the national level will further enhance the quality of medical care in Mongolia.