Conversion of forest to oil palm typically results in significant land changes within the soil, for example, extensive damage to the top soil, soil compaction and erosion. Such changes are often related to reductions within the biodiversity and abundance of the soil microbial communities. By using 16S rDNA and denaturing gradient gel electrophoresis, we investigated the microbial composition between oil palm plantations, at various stages of planting in mineral soil of Belaga, Sarawak in Malaysia, and forest ecosystem (biodiversity strip). Bacterial composition within biodiversity strips of secondary logged-over forests was mostly dominated by unclassified bacteria, Acidobacteria, and Actinobacteria followed by α-Proteobacteria whereas oil palm management areas were most commonly consisted of unclassified bacteria, Firmicutes, β-Proteobacteria, Actinobacteria, Acidobacteria and Chloroflexi. In a newly developed oil palm plantation, pH factor with the addition of fertiliser during land clearing altered the bacteria composition, affecting several phyla especially Acidobacteria, and with increasing pH, the population showed an abundance of Firmicutes, β-Proteobacteria, γ-Proteobacteria, Chloroflexi, and Bacteroidetes. Shifts in the bacterial community of the oil palm plantation, especially with the increasing number of the phylum Firmicutes, β-Proteobacteria, Bacteroidetes and the decreasing number of α-Proteobacteria caused by the slight increase of pH values indicated that changes of soil properties introduced by field management (e.g., fertiliser application) somehow affects bacterial composition. Nevertheless, the method of intercropping oil palm with black pepper and pineapple, during oil palm aged 4.5 years, showed increasing emergence of minor phyla from Gemmatimonadetes, Planctomycetes, Chlamydiae and Cyanobacteria, which contributes to the diverse variations of new phylum to the microbial diversity of the oil palm area indicating this method as a sustainable system for the oil palm management. Overall, there is a need for further research in using sustainable methods such as a suitable intercropping system that can positively improve soil fertility and a balanced long-term usage of biofertilisers and chemical fertilisers, which can enhance the biodiversity of the bacterial community and contributes to the sustainable development of oil palm plantations.