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At present in Thailand, biogas production ponds such as Covered Lagoon or Modified Covered Lagoon (MCL) systems are widely used for treating wastewater from cassava starch processing. However, it has been observed that the efficiency of these systems in producing biogas has decreased, falling below the designed capacity. This is because the internal environmental conditions within the system are unsuitable for microbial activity. It was found that the accumulation of total volatile acids (TVA) lowered the pH to levels that are unsuitable for methanogenic microorganisms. Moreover, the large capacity of the biogas production system (over 50,000 m³) may lead to inadequate wastewater distribution and limited interaction between the wastewater and microorganisms. Therefore, the main objective of this research is to improve the operating conditions in order to enhance the efficiency of the MCL biogas production system by operating it with careful consideration of wastewater feeding, appropriate organic loading rate (OLR), and hydraulic retention time (HRT). During the operational period, the MCL was fed with cassava starch processing wastewater at OLR of 0.2 kg-COD/m³/day and HRT of 38 days. This resulted in a COD removal efficiency >90% and stable operating conditions (alkalinity >1600 mg/L, TVA <300 mg/L, pH >6.9). Consequently, biogas production improved to over13,500 m³/day, with a methane content of 55–60%. Microbial community analysis revealed the presence of fermentation and organic matter degradation bacteria, particularly Aminicenantales sp. (4.31%), syntrophic fatty acid oxidation bacteria such as Syntrophus sp. (2.53%) and Smithella sp. (2.05%), as well as methanogenic populations, especially Methanosaeta sp. (9.51%), Methanobacterium sp. (2.07%), and Methanolinea sp. (1.78%).