The effect of soil amendment with biochar has been widely evaluated for its effects in mitigating greenhouse gas emissions (GHG) and remediating polluted soils with metals; however, a synergic understanding of the system, including biochar, soil, and microbial activity, is lacking. In this study, a meta-analysis of 854 paired data from 73 studies demonstrate that biochar application in soil affects GHG emissions and soil metal availability. First, several properties of biochar, soil, and microbial activity were considered as parameters in the meta-analysis. Then, the size effect was evaluated using the percentage of change (Pc) as obtained by the meta-analyzed data. Several parameters were related as influencer factors in GHG emissions and soil metal availability. Notably, biochar addition in soil resulted in a significant CO2 increase in emissions, whereas N2O emissions decreased; these results were directly correlated with microbial activity. Although this trend, demonstrated by the data analysis, differs from results of other studies found in the literature, it also emphasized the need for a deep understanding of the effect of biochar addition to soil (properties, nutrients, gas exchange, etc.) and to microorganisms (activity, diversity, etc.). Furthermore, it was also proved, that soil metal concentration decreases significantly when biochar was added (Cd > Zn > Pb > Cu > Fe). According to the results, biochar addition in soils contaminated with Cd and Cu was related to an increase in the microbial activity; while, soils amended with biochar but polluted with Pb, Zn, and Fe presented a higher inhibition effect on microorganisms. To improve the interpretation of soil amendment with biochar, it would be necessary to standardize the form for reporting results, particularly of the microbial activity and GHG emissions, in order to be used for future comparative studies.