Biochar production and incorporation into soil is gaining momentum as a sustainable strategy for climate change mitigation, supported by ever increasing reports of significant carbon (C) sequestration in soil and reduction in greenhouse gas (GHG) emissions from the amended soils. With the progression in biochar testing and use, there is also emerging evidence that biochar induces C sequestration in soil, and that it may not be solely caused by its inherent chemical stability, but also by the complex microbially driven processes and an increase in C use efficiency (CUE) through soil microbial metabolism. This evidence contradicts the current paradigm that sees the microbial CUE decrease during the degradation of recalcitrant material due to thermodynamic constraints, as observed only in several short-term and pilot-scale trials. As the CUE in soil results from interactions between several abiotic and biotic factors, in this paper we examine the link between the biochar properties, soil physico-chemical properties and microbial physiology to explain the CUE increase reported for biochar-amended soils. Based on the large body of physico-chemical literature, and on the high functional diversity and metabolic flexibility of soil microbial communities, we hypothesize that the long-term stabilization of biochar-borne C in the soil systems is not only controlled by its inherent recalcitrance, but also by the cooperative actions of improved soil status and increased microbial CUE. Given that the current knowledge on this specific aspect is still poor, in this feature paper we summarize the state of knowledge and examine the potential impact of biochar on some factors contributing to the whole-soil CUE. We conclude that, beside its inherent recalcitrance, biochar weathering and oxidation in soil create physical and chemical conditions that can potentially increase the microbial CUE. While these processes stabilize the microbial processed C in soil and increase soil fertility, more data from long-term field trials are needed to model the relationship between the CUE and the MRT of biochar-borne C. Based on our hypotheses and relying upon analysis of the available literature, we also suggest possible research approaches that may contribute to filling the gaps in the current knowledge on the topic.