The characteristics of Palm Oil Mill Effluent (POME) is a crucial factor affecting the yield and quality of biogas produced from anaerobic digestion. Hence, it is essential to understand how the operational processes and equipment in palm oil mills can affect POME characteristics and subsequently, biogas production efficiency. This study aims to evaluate the effects of different operating systems in four Palm Oil Mills (POM), including the usage of three-phase decanters, sludge separators, sludge recirculation, empty fruit bunch (EFB) press, water consumption, and sterilization systems, on POME characteristics such as chemical oxygen demand (COD), biological oxygen demand (BOD), total solids (TS), suspended solids (SS), pH, and oil and grease (OG). Experimental data was collected over a two-year period (from July 2019 to June 2021) at four POMs in Malaysia (A, B, C, and D). The ANOVA analysis showed that differences in the operational process flow and equipment led to significant variations in POME characteristics among the four mills. POM A was the only mill equipped with a three-phase decanter, which reduced the TS concentration in POME and recorded the lowest TS content (25,580 mg/L) compared to POM B, C, and D. However, the COD of POM A was still high due to the continuous addition of effluent from the empty fruit bunch (EFB) press station. POM B used a conventional cages system (CCS) for sterilization, whereas other POMs adopted a continuous sterilization (CS) system. POM B and D had the highest COD (more than 80,000 mg/L) due to low water consumption, absence of decanter, and direct discharge of sterilizer condensate to the sludge pit. POM C has achieved considerably lower TS content (29,144 mg/L) and the lowest COD level of 59,576 mg/L due to the highest water consumption. The hydrocyclone effluent from the kernel crushing plant (KCP) further diluted the POME in POM C. It is recommended to use sludge separators (instead of the three-phase decanter) and continuous sterilization system to produce desirable POME characteristics for maximum biogas generation. The water: FFB ratio should be kept below 1.2 m3/TFFB to maintain moderate COD, BOD, and TS content. This study provides essential information for POME biogas plant developers and POM owners to understand the mill process background and predict the POME qualities before designing an anaerobic digester or effluent treatment ponds.