A biotrickling filter (BTF) was designed for removal of sulfite (SO32−), sulfate (SO42−), and hydrosulfite (HSO−3) produced from ﬂue gas adsorbent during dual-alkali ﬂue gas desulfurization. With an SO32− concentration of 0.89 g-S/(L packing), BTF could completely remove SO32− within 3 h with an elimination capacity (EC) of 296 g-S/(m3h). With an SO42− concentration of 0.60 g-S/(L packing), the removal efficiency (RE) of SO42− reached 90.3% at 5.25 h and 95% at 24 h. With an HSO−3 concentration of 0.74 g-S/(L packing), HSO−3 could not be detected in the trickling liquid at 2 h with an EC of 370 g-S/(m3h). The difference in desulfurization performance of the BTF was minor when sodium lactate and sodium acetate were used as carbon sources. Acetate was more superior when taking both the carbon/sulfur ratio (C/S) and RE into account. The total dissolved sulfide yield was over 70% with sodium acetate as the carbon source, which was 15–20% higher than that with sodium lactate. Sodium lactate was not completely degraded and acetic acid was produced. All oxidation–reduction potential values were lower than −370 mV, indicating a perfect anaerobic condition in the BTF. The BTF could efficiently treat sulfite, sulfate, and hydrosulfite and could replace the regeneration stage of the dual-alkali process.