This retrospective study evaluated the influence of known risk factors on nonsurgical periodontal treatment (NSPT) response using a pocket depth fine-tuning multilevel linear model (MLM). Overall, 37 patients (24 males and 13 females) with moderate-to-severe chronic periodontitis underwent NSPT. Follow-up visits at 3, 6, and 12 months included measurements of several clinical periodontal parameters. Data were sourced from a previously reported database. In a total of 1416 initially affected sites (baseline PD ≥ 4 mm) on 536 teeth, probing depth (PD) and clinical attachment loss (CAL) reductions after NSPT were evaluated against known risk factors at 3 hierarchical levels (patient, tooth, and site). For each post-treatment follow-up, the variance component models fitted to evaluate the 3-level variance of PD and CAL decrease revealed that all levels contributed significantly to the overall variance (p < 0.001). Patients who underwent NSPT and were continually monitored had curative results. All 3 hierarchical levels included risk factors influencing the degree of PD and CAL reduction. Specifically, the type of tooth, surfaces involved, and tooth mobility site-level risk factors had the strongest impact on these reductions and were highly relevant for the success of NSPT.