Minimally invasive procedures were introduced in periodontics, which could enhance clinical outcomes and reduce post-operative discomfort. However, minimally invasive non-surgical periodontal therapy (MINST) as an alternative modality of conventional non-surgical root surface debridement has not been clearly evaluated by randomized controlled clinical trial. The present study aimed to investigate clinical outcomes and patients' comfort feedback of MINST compared to conventional non-surgical periodontal therapy (CNST). Patients with moderate to severe periodontitis were included. Nine out of ten patients were recruited and completed the post-treatment re-evaluation in this study. Randomized split-mouth design, CNST and MINST on each side, was performed. Clinical parameters, including periodontal probing depth (PD), gingival recession (REC), clinical attachment level (CAL), and gingival bleeding on probing (BOP), were recorded on baseline, 1 month and 3 months post-treatment. Non-parametric statistics were used for analysis. PD, REC, CAL, and BOP were improved after treatment in both CNST and MINST groups. Comfort feedback and gingival recession showed better outcomes in the MINST group than in the CNST group. No statistical significance of parameters was found between CNST and MINST. Within the limitations, minimally invasive non-surgical periodontal therapy could be an alternative modality of conventional non-surgical periodontal therapy. Further studies are required to establish clinical protocol and evidence of MINST.