Aim: To relate the clinical effects of two different forms of non-surgical periodontal therapy - scaling and root planing per quadrant (SRP-Q) and one-stage full-mouth disinfection (FMD) - to patient-based outcomes such as fear, anxiety, and pain of moderate chronic periodontitis patients. Methods: Dental Fear Survey (DFS) and Dental Anxiety Scale (DAS) questionnaires and Visual Analogue Scale (VAS) were applied to 78 patients randomized into two groups: SRP-Q (n = 37) and FMD (n = 41). Periodontal clinical parameters: probing pocket depth (PD), clinical attachment level (CAL), plaque index (PI), and gingival index (GI) were monitored at baseline and 6 months after treatment. Data were statistically analysed by chi-square, Fisher's exact, Mann-Whitney, Wilcoxon tests, Pearson's correlation, and Cluster analysis. Results: All periodontal clinical parameters improved from baseline to 6 months. Patients with higher fear and anxiety showed a worse clinical periodontal status before and after treatment (mean CAL, PI, and GI). After both types of treatment, fear and anxiety decreased (FMD: p = 0.019; SRP-Q: p = 0.043) with no differences between the groups. Pain did not differ between groups (FMD: 20.6 +/- 19.0 and SRP: 20.7 +/- 20.0; p = 0.930). Conclusions: In moderate chronic periodontitis patients, SRP-Q and FMD provided periodontal clinical improvements and similar experiences of fear, anxiety, and pain.