Synthetic hydrogels have been widely adopted as well-defined matrices for three-dimensional (3D) cell culture, with increasing interest in systems that enable the co-culture of multiple cell types for probing both cell-matrix and cell-cell interactions in studies of tissue regeneration and disease. We hypothesized that the unique dynamic covalent chemistry of self-healing hydrogels could be harnessed for not only the encapsulation and culture of human cells but also the subsequent construction of layered hydrogels for 3D co-cultures. To test this, we formed hydrogels using boronic acid-functionalized polymers and demonstrated their self-healing in the presence of physiologically-relevant cell culture media. Two model human cell lines, MDA-MB-231 breast cancer cells and CCL151 pulmonary fibroblasts, were encapsulated within these dynamic materials, and good viability was observed over time. Finally, self-healing of cut hydrogel 'blocks' laden with these different cell types was used to create layered hydrogels for the generation of a dynamic co-culture system. This work demonstrates the utility of self-healing materials for multi-dimensional cultures and establishes approaches broadly useful for a variety of biological applications.