Long-term treatment studies showed that the therapeutic effects of alendronate (ALN) were sustained over a 10-year treatment period. However, data on the effects on intrinsic bone material properties by long-term reduction of bone turnover are still sparse. We analyzed transiliacal bone biopsies of a subgroup of 30 Fracture Intervention Trial Long-Term Extension (FLEX) participants (n = 6 were treated for 10 years with ALN at dose of 10 mg/day, n = 10 were treated for 10 years with ALN at dose of 5 mg/day, and n = 14 were treated for 5 years with ALN plus a further 5 years with placebo) by quantitative backscattered electron imaging (qBEI) and scanning small-angle X-ray scattering (sSAXS) to determine the bone mineralization density distribution (BMDD) and the mineral particle thickness parameter T. BMDD data from these FLEX participants were compared with those from a previously published healthy population (n = 52). Compared with 5 years of ALN plus 5 years of placebo 10 years of ALN treatment (independent of the dose given) did not produce any difference in any of the BMDD parameters: The weighted mean (Ca(mean)), the typical calcium concentration (Ca(peak)), the heterogeneity of mineralization (Ca(width)), the percentage of low-mineralized bone areas (Ca(low)), and the portion of highly mineralized areas (Ca(high)) were not different for the patients who continued ALN from those who stopped ALN after 5 years. Moreover, no significant differences for any of the BMDD parameters between the FLEX participants and the healthy population could be observed. In none of the investigated cases were abnormally high mineralization or changes in mineral particle thickness observed (Ca(high) and T were both in the normal range). The findings of this study support the recommendation that antiresorptive treatment with ALN should be maintained for 5 years. Even with longer treatment durations of up to 10 years, though, no negative effects on bone matrix mineralization were observed.