In addition to energy recovery, the anaerobic digestion of agro-industrial byproducts can also produce different high-value-added compounds. Two-stage and single-stage reactors were compared for microbial communities’ selection and long-chain fatty acid (LCFA) accumulation to investigate which microbial genera are most linked to the production of these compounds. The microbial communities present in the two reactors’ configuration in the steady state were characterised by 16S rRNA amplicon sequencing, while LCFAs were extracted and quantified from digestate samples by gas chromatography. The results showed the differentiation of the microbially dominant families in the two setups: Defluviitaleaceae and Clostridiaceae in the acidogenic and methanogenic reactor of the two-stage reaction respectively, while Dysgonomonadaceae in the single-stage set-up. LCFA accumulation was significantly detected only in the acidogenic reactor, with palmitic (2764 mg/kg), linoleic (1795 mg/kg) and stearic (1751 mg/kg) acids as the most abundant. The dominance of Defluviitaleaceae UCG 011, along with the low abundance of the LCFA oxidiser Syntrophomonas spp. in the acidogenic reactor, could be linked to the accumulation of such compounds. Therefore, the different microbial communities shaped by the two reactors’ configuration affected the accumulation of LCFAs, indicating that the two-stage anaerobic digestion of agro-industrial byproducts was more effective than single-stage digestion.