In this study, tropical peat swamp soils from Giam Siak Kecil-Bukit Batu Biosphere Reserve (GSKBB) in Indonesia was evaluated to assess the impact of oil palm and rubber plantations on this unique organic soil through comparisons with soils from a natural forest using a polyphasic approach (chemical and molecular microbial assays). Changes in the ammonium, nitrate and phosphate concentration were observed in soils converted to agricultural use. Soil enzyme activities in plantation soils showed reduced β-glucosidase, cellobiohydrolase and acid phosphatase activities (50% - 55% decrease). PCR-DGGE based analysis showed that the soil bacterial community from agricultural soils exhibited the lowest similarity amongst the different microbial groups (fungi and Archaea) evaluated (34% similarity to the natural forest soil). Shannon Diversity index values showed that generally the conversion of tropical peatland natural forest to rubber plantation resulted in a greater impact on microbial diversity (ANOVA p < 0.05). Overall, this study indicated substantial shifts in the soil microbial activity and diversity upon conversion of natural peatland forest to agriculture, with a greater change being observed under rubber plantation compared to oil palm plantation. These findings provided important data for future peatland management by relating changes in the soil microbial community and activities associated to agricultural practices carried out on peatland.