Conductive materials have been applied to assist syntrophic metabolism in anaerobic digestion. However, their role in the transformation of organic compounds, particularly recalcitrant compounds, has not been revealed. In this study, iron-based materials - magnetite nanoparticles and Fe2+- were employed to explore their effects on the transformation of different organic matters in anaerobic system. Prompted methane production rates and quantity in iron-based materials groups were found due to the improved solubilization of organic particles, enhanced degradation of recalcitrant compounds, and maintained microbial activity under substrate-limited conditions. Specifically, the proportion of the reducing functional groups (C-C/H or CC) and O/C ratio were always significantly lower in iron-based materials supplemented groups (Fe groups) compared to Control group, despite hydrolysis was greatly enhanced in Fe groups. The greater dehydrogenation oxidation was confirmed in the presence of iron-based materials. The remaining humic-like substances (HS), a typical type of recalcitrant compound, was about 2.5 times higher in Control group (221.2 ± 5.3 mg/L-C) compared to Fe groups after 30 days degradation. By tracking the aromaticity of HS and individual compounds at molecular level, this study reveals that iron-based materials were more effective in stimulating the degradation of aliphatic moieties than the aromatic moieties of recalcitrant compounds. When readily biodegradable substrates were limited, Fe groups continued methane generation by using recalcitrant compounds (e.g. thiethylperazine and fluvoxamino acid) as carbon source, and the microbial activity was maintained according to higher relative abundance of protonated nitrogen and continuous methanogenesis activity at starvation phase.