Organic matter degradation and bacterial communities associated to the thermophilic phase of composting were compared using two different types of anaerobic digestates, one from a sewage sludge digester (SD), and the other from an agricultural digester (AD). The composting process exhibited similar variations in temperature, pH, moisture content and bacterial profiles, despite the inherent feedstock differences along with distinctive initial bacterial composition. According to the data obtained from 16S rRNA gene amplicon sequencing, SD constituted more than 20 bacterial phyla with Proteobacteria (21%) and Chloroflexi (21%) being predominant, meanwhile AD was represented by only 7 phyla in which Firmicutes was the most abundant phylum (73%). Nevertheless, bacterial community profiles of the two composting systems became more similarly represented at the phylum level, both dominated by Proteobacteria (65% in AD and 61% in SD), whereas Chromatiaceae and Sphingomonadaceae were the most abundant families in AD and SD, respectively. Highly diverse but similar bacterial communities were detected during the composting of different anaerobic digestates at the thermophilic phase.