This study presents a novel approach for the synthesis of biodegradable cell-laden microgels using stop-flow lithography (SFL), addressing critical challenges in the field of tissue engineering. Traditional methods for creating 3D cell cultures often rely on non-biodegradable materials, which limit their application and raise concerns about cell viability. In this work, we successfully replace poly(ethylene glycol) diacrylate (PEGDA) with dextran-2-hydroxyethyl methacrylate (dex-HEMA), a biocompatible and biodegradable alternative. Furthermore, we introduce a technical solution for sterile cell encapsulation, validated through assessments of cell growth and viability alongside the biodegradation rate of the microgel matrix. Our results demonstrate the potential of the self-assembly technique to form organized structures with high spatial resolution. By encapsulating relevant cell lines, Caco-2 and HT-29, within distinct microgel types, we pave the way for the development of sophisticated 3D co-culture models. These advancements hold significant promise for replicating the structural and functional complexities found in native tissues, thereby enhancing the relevance of in vitro studies in biomedical research.