Although the use of stem cell therapy for central nervous system (CNS) repair has shown considerable promise, it is still limited by the immediate death of a large fraction of transplanted cells owing to cell handling procedures, injection stress and host immune attack leading to poor therapeutic outcomes. Scaffolding cells in hydrogels is known to protect cells from such immediate death by shielding them from mechanical damage and by averting an immune attack after transplantation. Implanted hydrogels must eventually degrade and facilitate a safe integration of the graft with the surrounding host tissue. Hence, serial monitoring of hydrogel degradation in vivo is pivotal to optimize hydrogel compositions and overall therapeutic efficacy of the graft. We present here methods and protocols to use chemical exchange saturation transfer magnetic resonance imaging (CEST MRI) as a non-invasive, label-free imaging paradigm to monitor the degradation of composite hydrogels made up of thiolated gelatin (Gel-SH), thiolated hyaluronic acid (HA-SH), and poly (ethylene glycol) diacrylate (PEGDA), of which the stiffness and CEST contrast can be fine-tuned by simply varying the composite concentrations and mixing ratios. By individually labeling Gel-S and HA-S with two distinct near-infrared (NIR) dyes, multispectral monitoring of the relative degradation of the components can be used for long-term validation of the CEST MRI findings.