This retrospective study aimed to investigate the effect of known risk factors on nonsurgical periodontal treatment (NSPT) response using a pocket depth fine-tuning multilevel linear model (MLM). Thirty-seven patients (24 males and 13 females) with moderate to severe chronic periodontitis were treated with nonsurgical periodontal therapy. Follow-up visits at 3, 6, and 12 months included measurement of several clinical periodontal parameters. Data were extracted from a database system. Probing depth (PD) and Clinical Attachment Loss (CAL) reductions after NSPT in an overall of 1416 initially affected sites (baseline PD ≥ 4 mm), distributed on 536 teeth, were analyzed against known risk factors at three hierarchical levels (patient, tooth and site). The variance component models fitted to assess the three-level variance of PD and CAL decrease for each post-treatment follow-up showed that all levels contributed significantly to the overall variance (P < 0.001). Patients that underwent NSPT and were continually monitored had very curative results. All three hierarchical levels included risk factors who had impact on the to influence the magnitude of PD and CAL reduction. Specifically, the tooth’s type, surfaces involved and teeth mobility site-level risk factors showed the highest influence on these reductions, being highly relevant factors for the NSPT success.