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Background Afforestation of savannas in the Congolese coastal plains with eucalypt has provided wood pulp for industry and fuel energy for the local population. Typically, following afforestation, Acacia mangium are introduced to improve soil fertility and sustain productivity. Through investigations of particulate organic matter (POM), potential soil organic matter (SOM) quality was assessed in acacia and eucalypt plantations along rotations. Methods Nutrients in POM (4000-50 mu m) in the 0-5 cm soil layer were measured after five years into the second rotation (R2Y5) in relation to soil pH and P availability. Data were compared to those at the end of the first 7-year-rotation (R1Y7) and after two years into the second rotation (R2Y2) to evaluate overall SOM quality in the topsoil. Results At R2Y5, soil pH was higher in the pure eucalypt stands (100E) than in stands containing acacia, either in monoculture (100A) or evenly mixed with eucalypt (50A50E). Coarse POM (cPOM, 4000-250 mu m) beneath 100A had the highest N concentration (1.71%), followed by those beneath 50A50E (1.42%) and 100E (1.30%). Higher N was always found in the stands containing acacia. Lower sulphur (S) concentrations and P availabilities were observed in cPOM (50A50E). The greatest amount of coarse (414.7 g) and fine (214.5 g) forest floor litter were found in 100A stands, whereas higher C concentrations were found in the 100E stands for coarse forest floor litter (36.5%) and in the 50A50E stands for fine forest floor litter (38.7%). The decrease in cPOM N and C concentrations were lower than 20% (R1Y7) and 26% (R2Y5) relative to the younger stage (R2Y2). This tendency was more pronounced in fine POM (250-50 mu m) and organo-mineral fraction (< 50 mu m). Conclusions The main changes occurred in cPOM beneath stands containing acacia while higher weight of forest floor litter was found in 100A. Soil pH decreased in stands containing acacia. Overall N and C dynamics was enhanced in older stands (R2Y5) than in the younger stands (R2Y2). This may reveal a creation of more labile SOM with lower N and C concentrations in POM fractions in the surface layer, i.e., an ecosystem with a lower potential to mitigate climate change along rotations.