Background/Objectives: The objective assessment of natural tooth mobility remains challenging in clinical practice. This pilot study aimed to investigate the feasibility, repeatability, and agreement of a modified implant stability measurement system adapted for natural teeth using a custom-fabricated titanium bracket and a modified SmartPeg. Methods: Sixteen systemically healthy patients (10 males, six females) and 94 single-rooted permanent teeth with varying mobility grades were included. The tooth mobility was assessed using the Miller Mobility Index, Periotest M, and resonance frequency analysis (RFA) with the Osstell Beacon device. For the Osstell measurements, a custom titanium bracket bonded to the buccal tooth surface allowed for the placement of a modified SmartPeg. Each tooth was measured twice under standardized conditions, and mean values were recorded. The statistical analyses included Spearman correlation analysis, Cohen’s kappa for agreement with Miller categories, and intraclass correlation coefficients (ICCs) to assess the measurement repeatability. Results: The mean Periotest value was 12.70 ± 13.69, and the mean ISQ (implant stability quotient) value was 69.45 ± 19.37. The repeated measurements demonstrated excellent intra-examiner repeatability for both devices (ICC > 0.95). The Periotest values showed substantial agreement with the Miller mobility grades (κ = 0.763; p < 0.001), whereas the Osstell values demonstrated weak agreement with these ordinal categories (κ = 0.094; p = 0.048). A strong negative correlation was observed between the Periotest and Osstell measurements irrespective of the scales (r = −0.865; p < 0.001). Conclusions: In natural dentition, the resonance frequency analysis demonstrated reproducible measurements under controlled experimental conditions and showed measurable associations with conventional mobility assessments. However, the method remains investigational. The findings do not establish clinical validity for the routine assessment of natural tooth mobility. Further studies with larger sample sizes and statistical models accounting for patient-level clustering are required before clinical implementation can be considered. This study is registered at ClinicalTrials.gov (NCT07188168).