In Duchenne muscular dystrophy (DMD), diaphragm muscle dysfunction results in respiratory insufficiency, a leading cause of death in patients. Increased muscle stiffness occurs with buildup of fibrotic tissue, characterized by excessive accumulation of extracellular matrix (ECM) components such as collagen. However, changes in mechanical properties are not explained by collagen amount alone and we must consider the complex structure and mechanics of fibrotic tissue. The goals of our study were to (1) determine if and how collagen organization changes with the progression of DMD in diaphragm muscle tissue, and (2) predict how collagen organization influences the mechanical properties of ECM. We first visualized collagen structure with scanning electron microscopy (SEM) images and then developed an analysis framework to quantify collagen organization and generate image-based finite-element models. The image analysis revealed significant age- and disease-dependent increases in collagen fiber straightness and alignment, ranging from 4.7 to 13.4%, but collagen fibers retained a transverse orientation relative to muscle fibers. The mechanical models predicted significant age- and disease-dependent increases in transverse effective stiffness and average stress, ranging from 8.8 to 12.4%. Additionally, both healthy and diseased models revealed an increase in transverse stiffness relative to longitudinal stiffness, with significant age- and disease-dependent increases in the ratio of transverse to longitudinal stiffness, ranging from 19.7 to 24.5%. This study revealed changes in diaphragm ECM structure and mechanics during the progression of disease in the mdx muscular dystrophy mouse phenotype, highlighting the need to consider the role of collagen organization on diaphragm muscle function.