Tendon is an important mechanical tissue for musculoskeletal function and with a closely connected structure-function relationship. Molecules that make up a small portion of the tendon mass, such as small leucine-rich proteoglycans like decorin and biglycan, play crucial roles in collagen fibrillogenesis during development, maturity, aging, and healing. Isolated and systemic effects individually and jointly cause robust disruptions to the tendon composition, biology, and structure, often inhibiting the tissue’s ability to function properly. Analyses of these compositional and biological changes typically require ex vivo techniques with animal sacrifice or destruction of the tissue. Thus, in vivo evaluation of tendon is critical for longitudinal assessment. Microdialysis and photoacoustic ultrasound are promising techniques capable of assessing discrete changes in the tendon biological environment and composition. However, with the exception of photoacoustic imaging of hemoglobin, these assays have not been applied to rat tendon, in vivo. Therefore, the objectives of this study were comprised of two distinct, but interconnected goals. The first objective was to evaluate the differential roles of decorin and biglycan during healing of tendon injury in aged mice. The second objective was to adapt novel applications of photoacoustic ultrasound and microdialysis using acute injury as a model for extreme disruption to tendon homeostasis. Results suggest that biglycan has a larger role in the early phases of healing, while decorin is more pronounced at later time points in aged tendon, and both molecules are important for collagen fibrillogenesis and matrix assembly. Additionaly, this work demonstrates that microdialysis and photoacoustic ultrasound have the potential greatly enhance our understanding of mechanisms behind tendon healing through direct measurements of tendon biology, inflammation, and composition. This dissertation provides the groundwork for comprehensive in vivo analysis of tendon, thus increasing clinical translatability, reducing the total number of animals needed for future studies, and allowing for longitudinal analysis of tendon healing and disease progression on an individual basis.