Our results showed a decrease of the carbon and nitrogen content in soil amended with chemical fertilizers. Vermicompost amendment led to unchanged OC content, whereas the compost amendment increased the soils OC content compared to initial soil. The addition of earthworms reduced OC and N content in soils with organic amendments. This is in contrast to soil amended with mineral fertilizer only, where the presence of earthworms did not have any effect. Bioturbation influenced the lignin signature of the soils, and to a lesser extent the non-cellulosic carbohydrate signature. In conclusion, compost amendment combined with bioturbation influenced the quality and quantity of SOM and as result carbon storage and its biogeochemical cycling in tropical soils. Implications for soil fertility remain to be elucidated.