The production of biogas from sulfate-rich materials under anaerobic digestion results in the formation of hydrogen sulfide (H2S). The recommended level of H2S in the produced biogas for direct combustion purposes is in the range of 0.02 to 0.05% w/w (200 to 500 ppm), therefore, desulfurization is required to avoid damages to combustion equipment and prevent the formation of sulfur dioxide (SO2) which is an acid rain precursor. It has been well documented that physical, thermal, and chemical desulfurization approaches suffer from high operation costs as well as waste production needing to be disposed of. Accordingly, a great deal of efforts has been put into biological methods because of being more environmentally friendly and more economically advantageous in comparison with the other techniques. Biotrickling filtration (BTF) and microaerobic desulfurization have shown a high potential for H2S removal at pilot- and large-scale plants. Despite all the progress made and the promising aspects keeping these methods at the core of interest, there are still challenges to be addressed. The present article attempts to briefly review and discuss the challenges and future prospects of BTF and microaerobic desulfurization.