Dark fermentation (DF) is a simple method for hydrogen (H2) production through the valorization of various organic wastes that can be used as feedstock. In particular, an organic fraction of municipal solid waste (OFMSW) is a fermentation substrate that can easily be gathered and provides high yields in biogas and value-added organic compounds such as volatile fatty acids (VFAs). DF is coupled with a methanogenic reactor to enhance biogas production from the OFMSW. In this study, a two-stage reactor was conducted and monitored to optimize the methane yield by reducing the HRT at the DF reactor. A focus of the functional inference based on a next-generation sequence (NGS) metabarcoding analysis and comparison of microbial communities that populate each reactor stage was performed. Concerning gas quality, the two-stage system observed a hydrogen-rich biogas in the first fermentative reactor (on average 20.2%) and an improvement in the methane content in the second methanogenic digester, which shifted from 61.2% obtained for the one-stage experiment to 73.5%. Such increases were due to the improvement in substrate hydrolysis. As for the specific biogas production, the results showed an overall increase of 50%.