Alendronate therapy has been associated with serious side effects. Altering the alendronate concentration and combining with high-frequency loading as mechanical intervention was explored in this animal study as a treatment for osteoporosis. The bone anabolic potency of high-frequency loading was overruled by the different alendronate dosages applied in the present study. Further exploration of reduced hormonal therapy associated with mechanical interventions in osteoporosis treatment should be sought. The aim of the present study was to investigate the effect of alendronate (ALN) administration at two different dosages, associated or not with high-frequency (HF) loading, on the bone microstructural response. Sixty-four female Wistar rats were used, of which 48 were ovariectomized (OVX) and 16 were sham-operated (shOVX). The OVX animals were divided into three groups: two groups were treated with alendronate, at a dosage of 2 mg/kg (ALN((2))) or at a reduced dosage of 1 mg/kg (ALN((1))) three times per week. A third OVX group did not receive pharmaceutical treatment. All four groups were mechanically stimulated via whole body vibration (WBV) at HF (up to 150 Hz) or left untreated (shWBV). ALN and HF were administered for 6 weeks, starting at 10-week post-(sh)OVX. Tibia bone structural parameters were analyzed using ex vivo microcomputed tomography. Trabecular bone loss and structural deterioration resulting from ovariectomy were partially restored by ALN administration, demonstrated by the improvement of trabecular patter factor (Tb.Pf), trabecular separation (Tb.Sp), and structure model index (SMI) of the ALN groups compared to that of the OVX group, regardless of the applied dosage [ALN((2)) or ALN((1))] or mechanical loading regime (shWBV or WBV). However, a significant positive effect of the ALN((1)) administration on trabecular (decrease of Tb.Sp and SMI) and cortical bone (increase of cortical thickness) microarchitecture compared to that of the OVX status group was observed for both loading regimes was not seen for ALN((2)). Furthermore, HF loading resulted in cortical bone changes, with an increased trabeculary area and endocortical perimeter. Finally, the benefits of a combined therapy of ALN with HF loading could not be discerned in the present experimental conditions. The bone anabolic potency of HF loading was overruled by the ALN dosages applied in the present study. Further altering the ALN dosage combined with robust mechanical stimuli needs to be considered in osteoporosis research and eventually therapy.