It is currently unclear whether trace elements (TEs) deficiency is due to low bioavailability or low absolute TEs concentrations, especially in high-pH anaerobic digestion (AD) systems. A mixed solution of TEs and EDTA-Na2 were used separately in mono-AD of chicken manure (CM) leachate to investigate this research gap. The results showed relatively low bioavailability of Fe, Mn, and Zn. The bioavailability of all TEs remained stable along with a gradual increase in total ammonia nitrogen concentration. Both TE and EDTA-Na2 supplementation improved the bioavailability of TEs, but TEs supplementation also gave a high proportion of soluble TEs. Adding TEs improved methane production efficiency (+38.3%) and decreased the H2S content. The exchangeable fraction of specific TE (Mo) in H2/CO2 pathway was higher in the TEs treatment. TEs bioavailability and absolute concentrations of available TEs are critical aspects that need to be scrutinized to assess the risk of TEs deficiency.