Effects on bone material properties of two-year antiosteoporotic treatment were assessed using in vivo impact microindentation (IMI) in patients with low bone mineral density (BMD) values. Antiresorptive treatment, in contrast to vitamin D ± calcium treatment alone, induced BMD-independent increases in bone material strength index, measured by IMI, the magnitude of which depended on pretreatment values. Introduction Bone material strength index (BMSi), measured by IMI in vivo, is reduced in patients with fragility fractures, but there is no information about changes in values during long-term therapy. In the present study, we assessed changes in BMSi in patients receiving antiosteoporotic treatments for periods longer than 12 months. Methods We included treatment-naive patients with low bone mass who had a BMSi measurement with OsteoProbe® at presentation and consented to a repeat measurement after treatment. Results We studied 54 patients (34 women), median age 58 years, of whom 30 were treated with bisphosphonates or denosumab (treatment group) and 24 with vitamin D ± calcium alone (control group). There were no differences in clinical characteristics between the two groups with the exception of a higher number of previous fragility fractures in the treatment group. Baseline hip BMD and BMSi values were lower in the treatment group. After 23.1 ± 6.6 months, BMSi increased significantly in the treatment group (82.4 ± 4.3 vs 79.3 ± 4.1; p < 0.001), but did not change in the control group (81.5 ± 5.2 vs 82.2 ± 4.1; p = 0.35). Changes in BMSi with antiresorptives were inversely related with baseline values (r = − 0.43; p = 0.02) but not with changes in BMD. Two patients in the control group with large decreases in BMSi values sustained incident fractures. Conclusion In patients at increased fracture risk, antiresorptive treatments induced BMD-independent increases in BMSi values, the magnitude of which depended on pretreatment values.