Biomass wastes originating from palm oil milling activities can be characterized by their high biochemical oxygen demand (BOD), chemical oxygen demand (COD), total suspended solid (TSS), and oil and grease content. The utilization of oil palm wastes such as palm oil mill effluent (POME) and empty fruit bunch (EFB) has great potential for a sustainable energy biomass pellet as it reduces the reliance on conventional materials for energy production. A mixture of POME and EFB in various ratios ranging between 7:3, 8:2, 9:1, and 10:0 was fermented in the presence of Lysinibacillus sp. LC 556247 for 120 h at 37 ± 2 °C and 180 rpm with the aim of elucidating the biodegradation of complex organic material in terms of BOD, COD, TSS, total organic carbon, inorganic carbon, and total carbon content. After fermentation, the mixtures were oven dried at 105 °C overnight and then subjected to calorific energy value (CEV) determination. The highest CEV of 20.26 MJ/kg was achieved for a ratio of 10:0 (slightly higher than the control experiment with the value of 18.67 MJ/kg), with maximum removal efficiencies of COD (12.19%), BOD (11.72%), TSS (93.94%), and oil reduction of 17.43%. The addition of EFB did not positively increase the CEV.