Global expectation for sustainability has prompted the transition of practices in wastewater treatment plants toward not only waste management but also energy and nutrient recovery. It has been shown that low-temperature hydrotherm (HT) treatment can enhance downstream biogas production via anaerobic digestion (AD). Yet, because the application of combined HT and AD is still at an early stage, a systematic understanding of the dynamic speciation evolution of important elements is still lacking. This study investigates energy and nutrient recovery from sewage sludge and swine manure via combined HT-AD treatment. Bench-scale investigation was conducted to evaluate biogas production and understand the dynamic evolution of organic carbon (C) and phosphorus (P) speciation. C and P speciations were characterized using complementary chemical and spectroscopic techniques, including 13C nuclear magnetic resonance (NMR) spectroscopy, P X-ray absorption near edge structure (XANES) spectroscopy, and sequential chemical extraction. Results from this study suggest that low-temperature HT pretreatment can achieve enhanced biogas production for sludge compared to the minimal effect on the biogas production from manure. It also provides guidance for P recovery from liquid digestate and solid residue after the AD process.