Compared to pyrolysis biochar (PBC), gasification biochar (GBC) differs in both composition and surface functionalities due to the use of an oxidizing purging gas. This work compares the effect of using PBC and GBC as soil amendments on the soil properties, trace metal bioavailability, soil microbial activity, and soil dissolved organic matter (DOM). Biochar-driven reduction of bioavailable metals does not necessarily result in a positive impact on the soil microbial growth. The DOM in the soil was strongly related to the soil microbial activity, as revealed by the strong correlation between the soil dehydrogenase activity (DHA) and soil dissolved organic carbon (r = 0.957, p < 0.01). Three identified fluorescent components (C1, C2, C3) in the soil DOM were closely associated with the soil microbial activity, for instance, with a clear positive correlation between the soil DHA and Cl (r = 0.718, p < 0.05) and a significant negative correlation between the total bacterial fatty acid methyl ester content and C3 (r = -0.768, p < 0.05). The bioavailability of Cd and Zn is not only related to the pH and surface functionalities of the biochar, but also to its aromatic carbon and inorganic mineral composition. This study further demonstrates that a fluorescence excitation-emission matrix coupled with parallel factor analysis is a useful tool to monitor changes in the soil quality after application of biochar, which is greatly relevant to the soil biota.