This study demonstrates a new strategy for the development of a three-dimensional (3D) cell culture model-based cellular biosensing system. Distinctly different from the previously reported layering or separating fabrication of cell culture and sensing devices, herein living cells and enzymes as sensing elements are immobilized into a dipeptide-derived hydrogel matrix through simple one-pot self-assembly. The cells are then 3D cultured in the functional hydrogel, and the releasing superoxide anion (O2•-) is detected in situ by a cascade superoxide dismutase and horseradish peroxidase-based electrochemical biosensor. This novel design provides considerable advantages, including the possibility of capturing molecular signals immediately after they are secreted from living cells, due to the close proximity of the enzymes and the O2•--producing cells. Furthermore, incorporating all components in a 3D matrix provides a confinement environment, that can lead to a concentrating effect of analysts. These properties allow the sensing device to achieve ultrahigh sensitivity and a precise response to a very low number of O2•- molecules. The proposed approach, based on the self-assembly of a small molecular hydrogel, also simplifies experimental procedures and increases protocol flexibility to cell culture methodology and sensing design. Consequently, this novel 3D culture model-based cellular biosensing system is envisaged to be useful for cellular function and pathology, drug discovery, and toxicity studies.