The use of organic matter (OM) amendments is widespread in tropical countries and may be beneficial for soil carbon storage. Interactions between earthworms and OM amendments in tropical soils are largely unknown. The aim of this study was to investigate the effect of bioturbation on the quantity and chemical composition of OM in soil amended with compost and vermicompost. Our approach included comparison of soil samples amended with compost, vermicompost or chemical fertilizers in the presence or absence of earthworms during a one-year greenhouse experiment. The soils were submitted to a regular cultivation cycle. After one year, we analysed bulk samples for soil OM elemental composition and characterised its lignin and non-cellulosic carbohydrate components. 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.