Amendment of recalcitrant organic materials with high carbon/nitrogen (C/N)-ratio may improve and maintain soil labile C for a longer period, thus enhancing the productivity of soils with low fertility; however, immobilization of N may affect the plant growth negatively. To reduce the negative impacts, recalcitrant organic materials can be pre-incubated with N-rich sources or applied in combination with fertilizers. The current study evaluated sawdust biochar (BC) and pre-incubated cattle manure–sawdust mixture (CS) amendments with synthetic fertilizers in improving soil carbon pool, soil fertility and maize (Zea mays L.) yield on a tropical Alfisol. Four treatments: control, site-specific fertilizer (SSF), site-specific fertilizer with sawdust biochar (BC + SSF) or pre-incubated cattle manure-sawdust mixture (CS + SSF), were evaluated for two seasons with maize. The residual effect was evaluated in the third season. During the year of active C application, lability index, C management index and potentially mineralizable N were significantly greater in CS + SSF than BC + SSF treatment. However, the same indices measured in the third season with no further application of amendments were significantly greater in BC + SSF than in CS + SSF treatment, indicating an increase in more recalcitrant C pool with BC amendment. Application of organic amendments improved soil fertility parameters compared with the application of fertilizer alone. Maize yield was significantly increased by fertilizer, with or without organic amendments; with significantly greater yield in BC + SSF than other treatments. Results suggest that soil amendment with BC had greater potential to improve the soil carbon pool and maintain labile carbon for a longer period than a pre-incubated CS.