Oil palm (Elaeis guineensis Jacq.) has been cited as the main raw material for biodiesel production in Brazil. This oilseed is cultivated in the Brazilian Atlantic coast in mixed ‘spontaneous’ agroforest systems and in commercial plantations. Different oil palm cultivations derived from native rain forest can modify the soil organic carbon (C) dynamics. The aim of our study was to evaluate the changes in soil organic carbon (SOC) stocks after conversion of Atlantic forest into oil palm production in Bahia State, Brazil. Soil samplings were carried out in May 2008 and February 2009 in four areas: Native Atlantic Rain Forest (NARF), a mixed secondary forest/agroforestry Spontaneous System (SPSY), oil palm cultivated during 23 (OP23) and 34 years (OP34). The spatial variability of C and nitrogen (N) contents and the differences in soil C stocks between the avenues (inter-rows) and frond piles in oil palm areas were evaluated. We found the highest soil C contents in the region next the oil palm base (1.22% in OP23 and 1.49% in OP34). The soil C stocks were higher in frond piles (1.7 times in OP23 and 2.6 times in OP34) than in the avenues, due to inputs of soil organic matter by pruned fronds. The soil C stocks adjusted for a mass equivalent and different clay content decreased in SPSY. The OP23 area showed lower SOC stocks compared with native system. However, OP34 area showed the highest C stocks among the areas evaluated with an increase of 25% of the amount of SOC storage found under native vegetation. We found SOC storage of 34.7 Mg ha−1 and 66.6 Mg ha−1 under OP23 and OP34, respectively, indicating an increase of soil C stocks in oil palm plantations over time.