Collagen is the major component of connective tissues, where it assembles into fibrils that exhibit various sizes and form various 3D structures depending on the observed tissue. Any disruption of this microstructure is associated with tissue malfunction and defective biomechanical properties. This study thus aims to investigate the relationship between the microstructure and the macroscopic mechanical response of typical connective tissues: skin (disordered) and cornea (highly ordered). To overcome technical issues in providing experimental multiscale data in intact tissues, we have implemented an original setup combining mechanical assays at tissue scale and Second Harmonic Generation (SHG) imaging of collagen reorganization. This multiphoton imaging modality represents an effective structural probe of the micrometer-scale collagen organization in unstained tissues. 3D SHG images were acquired in dermis from ex vivo murine skin biopsies during controlled stretching until rupture, and in ex vivo Human cornea during inflation assays. Specific image processing was implemented to quantify the reorganization of tissue microstructure and correlate it with stress/stretch relationship at macroscopic scale. In murine skin, we showed that the collagen fibers continuously aligned with stretch, generating the observed increase in mechanical stress, which challenges the usual theoretical explanation of the microstructural origin of the skin macroscopic mechanical response. Moreover, dermis from transgenic mice with defective collagen microstructure exhibited altered collagen reorganization upon traction, which could be linked to the microstructural modifications. In Human cornea, our results showed no reorganization of the collagen fibrils at sub-micrometer scale within the stromal lamellae, while the lamellae at micrometer scale reorganized in a more balanced way along 2 main perpendicular directions, in line with the deformation observed at the macroscopic scale. In conclusion, our approach provides an efficient tool to investigate the biomechanics of collagen-rich tissues in normal and pathological context and to guide tissue engineering with appropriate biomechanical responses.