Biofilm samples (~5 g of electrode material per sample) were collected from the anode (graphite felt) or cathode (nickel foam) of an electrofermentation reactor (EFR) or electromethanogenic reactor (EMR) at day 256 of operation, resuspended in sterile water, and processed at the Unidad Universitaria de Secuenciacion Masiva y Bioinformatica (UUSMB), Instituto de Biotecnologia, UNAM. Genomic DNA was extracted with the DNeasy PowerSoil Kit (Qiagen). The V3-V4 region of the 16S rRNA gene was amplified with the Klindworth et al. (2013) primer pair 341F/805R carrying Illumina sequencing-adapter overhangs, using KAPA HiFi HotStart ReadyMix (Roche), following the Illumina 16S Metagenomic Sequencing Library Preparation protocol (Illumina, Part No. 15044223). Dual indices were added with the Nextera XT Index Kit (Illumina, FC-131-1002). Libraries were sequenced on an Illumina MiSeq platform with the v3 reagent kit (600 cycles) in a paired-end 2x300 bp configuration. Raw R1 and R2 reads were no longer available; paired-end reads had been merged with FLASH v1.2.7 prior to deposition. Only the FLASH-merged extendedFrags FASTQ files are provided here (single-end format).