As oil palm has been considered one of the most favorable oilseeds for biodiesel production in Brazil, it is important to understand how cultivation of this perennial crop will affect the dynamics of soil organic carbon (SOC) in the long term. The aim of this study was to evaluate the changes in soil C stocks after the conversion of forest and pasture into oil palm production in the Amazon Region. Soil samples were collected in March 2008 and September 2009 in five areas: native forest (NARF), pasture cultivated for 55 years (PAST), and oil palm cultivated for 4 (OP-4), 8 (OP-8) and 25 years (OP-25), respectively. Soils were sampled in March 2008 to evaluate the spatial variability of SOC and nitrogen (N) contents in relation to the spacing between trees. In September 2009, soils were sampled to evaluate the soil C stocks in the avenues (inter rows) and frond piles, and to compare the total C stocks with natural forest and pasture system. Soil C contents were 22-38% higher in the area nearest the oil palm base (0.6 m) than the average across the inter row (0-4.5 m from the tree), indicating that the increment in soil organic matter (SOM) must have been largely derived from root material. The soil C stocks under palm frond piles were 9-26% higher than in the inter rows, due to inputs of SOM by pruned palm fronds. The soil carbon stocks in oil palm areas, after adjustments for differences in bulk density and clay content across treatments, were 35-46% lower than pasture soil C stocks, but were 0-18% higher than the native forest soil C content. The results found here may be used to improve the life cycle assessment of biodiesel derived from palm oil.