Glucocorticoid induced osteoporosis (GIOP) is the most common negative consequence of long-term glucocorticoid treatment, leading to increased fracture risk followed by loss of mobility and high mortality risk. These biologically induced changes in bone quality at molecular level lead to changes both in bone matrix architecture and bone matrix composition. However, the quantitative details of changes in bone quality - and especially their link to reduced macroscale mechanical properties are still largely missing. In this study, a mouse model for glucocorticoid-induced osteoporosis (GIOP) was used to investigate mechanical and material alterations in bone cortex (natural nanocomposite) at different scale. By combining quantitative backscattered electron (qBSE) imaging, nanoindentation and high brilliance synchrotron X-ray nanomechanical imaging on a genetically modified mouse model of GIOP, we were able to quantify the local indentation modulus, mineralization distribution and the alterations of nanoscale structures and deformation mechanisms in the mid-diaphysis of femur, and relate them to the macroscopic mechanical changes. Our results showed clear and significant changes in terms of material quality of bone at nanoscale and microscale, which manifests itself in development of spatial heterogeneities in mineralization and indentation moduli across the bone organ, with potential implications for increased fracture risk.