Currently, the existence of a gut–bone axis receives massive attention, and while sound premises and indirect proofs exist for the gut–bone axis concept, few studies have provided actual data linking the gut and bone physically. This study aimed to exploit the versatile nature of nuclear magnetic resonance (NMR) to link NMR relaxometry data on bone mineralization with NMR spectroscopic profiling of gut metabolites. For this purpose, sample material was obtained from a 6-week intervention study with ovariectomized (OVX) rats (n = 49) fed with seven different diets varying in calcium content (0.2–6.0 mg/kg) and prebiotic fiber content (0–5.0% w/w). This design ensured a span in (i) calcium available for bone mineralization and (ii) metabolic activity in the gut. After termination of the intervention, longitudinal (T₁), transverse (T₂) relaxation, and mechanical bone strength were measured on the excised femur bones. A PLS model with high predictability (Q² = 0.86, R² = 0.997) was demonstrated between T₂ decay curves and femur mechanical strength. Correlations were established between bone T₂ populations and gut short-chain fatty acids. In conclusion, the present dual NMR approach showed strong correlation between T₂ relaxation and mechanical strength of the bone, and when metabolic activity in the gut was modulated by inulin, the potential existence of a gut–bone axis was demonstrated.