Cell therapies have the potential to slow the progression of painful intervertebral disc (IVD) degeneration, which is a leading cause of global disability. There are two major challenges preventing clinical translation of IVD cell therapies:​ (1) lack of cell delivery biomaterials capable of balancing the biomechanical and biological demands of the loaded IVD environment and (2) poor understanding of the heterogeneous cell types within the IVD to motivate optimal cell sources. This thesis addresses both challenges by (1) engineering a novel, minimally invasive, composite cell delivery biomaterial for annulus fibrosus (AF) repair and (2) developing a comprehensive single-cell RNA-sequencing (scRNA-seq) atlas of the bovine caudal IVD. Part I of this work first found that AF cells seeded within high-modulus genipin-crosslinked fibrin (FibGen) undergo apoptosis because of acute crosslinker cytotoxicity and poor cell-biomaterial binding. To overcome these mechanisms of cell death, AF cells were microencapsulated in oxidized alginate (OxAlg) microbeads (MBs) prior to FibGen seeding to form FibGen+MB composites. Conceptually, OxAlg MBs formed a physiochemical barrier to genipin molecules and RGD-functionalized OxAlg MBs (MB-RGD) enhanced cell-biomaterial binding. Cell-laden FibGen+MB-RGD composites were evaluated ex vivo using long-term large animal IVD organ culture under dynamic physiological loading, which showed that this strategy provides immediate biomechanical stabilization and allows the controlled release of cells for long-term healing. Part II of this work applied scRNA-seq to the IVD to understand heterogeneous cell types and motivate cell choices for cell delivery applications. Downstream analyses identified novel cell populations not typically found in the IVD, discovered novel markers for the nucleus pulposus (NP), inner AF (iAF) and outer AF (oAF), and showed that NP and oAF subpopulations support cell survival under physiological IVD stresses or extracellular matrix (ECM) synthesis. Lastly, single-cell transcriptional entropy and pseudotime analyses provided evidence for NP and oAF progenitor cell populations. Taken together, this new knowledge advances the field of AF tissue engineering by developing a novel composite biomaterial and informing optimal cell sources for AF cell delivery. Results of this work will likely be broadly applicable to engineering other musculoskeletal soft tissues that experience high mechanical demands and have poor endogenous healing capacity.