The influence of periodontal phenotype (PP) has been documented in the outcomes of various surgical periodontal interventions such as crown lengthening, mucogingival surgery, implant restoration, and open flap debridement. Previous studies with smaller sample sizes have assessed the role of PP on the outcome of nonsurgical periodontal therapy with inconsistent results. The aim of the current interventional study is to estimate the influence of PP on the outcome of subgingival instrumentation in Stage II and III, Grade A and B periodontitis. Fifty-two patients (n = 27 thick PP and n = 25 thin PP) underwent subgingival instrumentation using ultrasonic scalers and curettes under local anesthesia in a single sitting, and periodontal parameters were recorded at baseline, 2, 4, and 6 months. The McNemar and Chi-square tests were applied for categorical data, whereas the Wilcoxon signed-rank test and Mann-Whitney U-test were applied for continuous data in intra- and intergroup comparisons, respectively. Significantly better improvements in deeper pockets (>5 mm) with thick PP were observed. Loss of attachment was found in thin, bleeding on probing (BOP)-negative sites with an initial probing depth of ≤3 mm. However, BOP-positive sites belonging to both groups exhibited higher improvements in terms of clinical parameters. Probing depth, PP, and periodontal inflammation recorded in terms of BOP influence the gain in clinical attachment following subgingival instrumentation.