Clinical tools for evaluating fracture risk, such as dual energy X-ray absorptiometry (DXA) and quantitative ultrasound (QUS), focus on bone mineral and cannot detect changes in the collagen matrix that affect bone mechanical properties. However, the mechanical response tissue analyzer (MRTA) directly measures a whole bone mechanical property. The aims of our study were to investigate the changes in fatigue resistance after collagen degradation and to determine if clinical tools can detect changes in bone mechanical properties due to fatigue. Male and female emu tibiae were endocortically treated with 1 M KOH for 1-14 days and then either fatigued to failure or fatigued to induce stiffness loss without fracture. Partial fatigue testing caused a decrease in modulus measured by mechanical testing even when not treated with KOH, which was detected by MRTA. At high stresses, only KOH-treated samples had a lower fatigue resistance compared to untreated bones for both sexes. No differences were observed in fatigue behavior at low stresses for all groups. KOH treatment is hypothesized to have changed the collagen structure in situ and adversely affected the bone. Cyclic creep may be an important mechanism in the fast deterioration rate of KOH-treated bones, as creep is the major cause of fatigue failure for bones loaded at high stresses. Therefore, collagen degradation caused by KOH treatment may be responsible for the observed altered fatigue behavior at high stresses, since collagen is responsible for the creep behavior in bone.