Abstract: Anaerobic digestate derived from antibiotic-producing bacterial residues poses severe environmental risks due to the persistent accumulation of residual antibiotics, antibiotic resistance genes (ARGs), and undegraded organic contaminants. To address these hazards while promoting high-value resource recovery, this study developed a microwave-assisted hydrothermal carbonization (HTC) process to treat digestates obtained from both the single anaerobic digestion of gentamicin-producing bacterial residues (GBR) and the co-anaerobic digestion of GBR with corn stover (CS). The physicochemical properties, structural characteristics, ARG elimination, and nitrogen retention behavior of the resulting hydrochars were systematically investigated. Initial composition analysis revealed that co-anaerobic digestion effectively enhanced the degradation of cellulose and hemicellulose. However, approximately 50 wt% of lignocellulose remained in the digestate, highlighting substantial potential for downstream carbonization and energetic conversion. Following microwave-assisted HTC, the hydrochars exhibited significantly decreased volatile matter, increased fixed carbon content, and elevated degrees of aromatization and carbonization. Under optimal reaction conditions of 160 °C for 90 min, the hydrochar produced from the co-fermented digestate achieved a higher heating value of 17.13 MJ/kg with a high energy yield of 88.22%. Compared with hydrochars from the single-digestate treatment, the co-fermented hydrochar possessed a superior specific surface area, an expanded total pore volume, and a higher abundance of oxygen-containing surface functional groups, thereby enhancing its potential as an effective adsorbent. Furthermore, microwave-assisted HTC demonstrated remarkable performance in biological risk mitigation, achieving a 98.40% total reduction rate in target ARGs at 180 °C for 120 min. Meanwhile, nitrogen in the hydrochar remained predominantly in organic forms, with a maximum total nitrogen retention of 23.58 mg/g recorded at 160 °C for 90 min. Overall, coupling co-anaerobic digestion with microwave-assisted HTC provides an effective integrated framework for simultaneously detoxifying hazardous antibiotic residues, sequestering carbon, and conserving valuable nutrient nitrogen. This work offers an innovative technology and theoretical basis for transforming hazardous industrial biowastes into multi-functional hydrochar materials suitable for solid fuel, environmental remediation, and sustainable agricultural soil amendment.