Stem cell transplantation has emerged as a promising strategy for the treatment of traumatic injury and degenerative diseases. While direct cell injection at the wound site is clinically favored due to its minimal invasiveness, low levels of transplanted cell survival and retention limit functional recovery. By encapsulating stem cells within either natural biopolymer hydrogels such as alginate, collagen, and Matrigel or engineered biomaterials such as MITCH, we may improve cell viability by providing biomechanical protection, biochemical survival cues, and/or cytocompatible scaffolds for cell adhesion. Using microfluidics to create a controlled in vitro model of cell injection, we are currently investigating the mechanical disruption of hydrogel encapsulated cells during syringe flow to isolate points of cell damage and to establish design principles for protective injectable scaffolds.