Hydrogel bioelectronics are promising candidates to bridge biological and electronic systems. However, maintaining stable communication between hydrogel devices and biological materials in wet physiological environments is challenging owing to the swelling-induced mechanical degradation of hydrogel encapsulation and electrical failure of conductive networks. To address this, we report a micellar self-assembly method to fabricate soft, stretchable and anti-swelling hydrogels as building blocks for implantable hydrogel bioelectronics. Compared with conventional swelling hydrogels and silicones, these anti-swelling hydrogels show reduced foreign-body reactions during long-term implantation. Using a microgel strategy, we engineer the anti-swelling hydrogel into a supporting matrix and a biphasic conductive hydrogel ink, enabling embedded 3D printing of hydrogel bioelectronics. Through regulating the monomer diffusion during the manufacturing process, we tailor the conductive phase of the conductive hydrogel, achieving conductivities of up to 4,000 S cm−1, and a strain at electrical failure exceeding 1,300% when equilibrated in an aqueous environment. Different types of hydrogel bioelectronic implant are printed, including brain–computer interfaces, wirelessly powered optoelectronics and sciatic-nerve stimulators. These devices show long-term stability and reliable operation following implantation in rats.