This longitudinal study aimed to compare the association between gingival phenotype (thin vs. thick) and periodontal disease severity in patients undergoing fixed orthodontic therapy (FOT) and Invisalign treatment over a six-month follow-up period. Clinical periodontal parameters, including full mouth plaque score (FMPS), full mouth bleeding score (FMBS), gingival index (GI), probing pocket depth (PPD), clinical attachment loss (CAL), gingival recession (GR), keratinized tissue width (KTW), transgingival probing, and gingival biotype assessment, were recorded at baseline and 6 months into treatment for both orthodontic groups and a control group. Statistical analysis evaluated differences in parameters between groups and across time points. In the thick phenotype, both Invisalign and FOT groups showed a significant mean reduction in FMPS (baseline to 6 months) by -24.8707 and -12.3489, respectively (p < 0.05). The gingival index decreased significantly for both groups, with Invisalign and FOT showing reductions of -0.83355 and -1.10409, respectively (p < 0.05). FMBS (baseline to 6 months) decreased significantly for Invisalign and FOT, with mean differences of -9.10298 and -12.6579 (p < 0.05). Probing pocket depth (baseline to 6 months) was also significantly reduced for both Invisalign and FOT groups while CAL showed non-significant differences in both groups (p > 0.05). Similar changes were seen in the thin phenotype too. This study highlights the positive influence of both Invisalign and fixed orthodontic therapy on periodontal health, particularly in patients with thin and thick gingival biotypes. These findings, with significant reductions in key periodontal parameters, offer valuable insights to guide orthodontic treatment decisions and enhance patient outcomes.