Biochar affects soil carbon (C) dynamics via shifting microbial community, but the active bacteria that regulate the rhizosphere-based C cycling remain to be identified. Here, a continuous 13CO2 labeling pot (Zea mays L.) experiment over 14 days, combined with RNA-based stable isotope probing (RNA-SIP), were used to characterize the active bacterial communities involved in the mineralization of rhizodeposits and soil organic C (SOC) in biochar-amended soil. Compared with the non-amended soil, biochar shifted the rhizosphere communities towards having lower richness and evenness, and particularly stimulated the growth of Actinobacteria (e.g., genus affiliated to Micrococcaceae) and other oligotrophs, most likely due to neutralizing soil acidity (from 4.53 to 6.17) and increasing content of recalcitrant organic C (from 10.69 to 25.77 g·kg−1). These enriched genera were associated with mineralization of both rhizodeposits and SOC, giving 35.09% and 87.28% increased mineralization of rhizodeposits and SOC. This led to much less (by 58.50% decrease) incorporation of 13C into biochar-amended soil. This study deciphered the active microorganisms in the biochar-soil–plant system that likely increased SOC and rhizodeposit mineralization (fewer rhizodeposits remaining), and thus diminished C sequestration by biochar per se.