Introduction: Periodontitis is a chronic disease of the supporting apparatus of teeth which affects more than 700 million people. Non-surgical periodontal therapy (NSPT) is the gold standard that is effective in controlling the infection. Although NSPT significantly reduces the number of periodontal pathogens, re-establishment of the original periodontopathogen flora may occur shortly thereafter. In addition to initial therapy, additional or alternative methods are used, such as the use of systemic and local antibiotics, antiseptics, and disinfectants. Due to the increasing bacterial resistance to antibiotics and antiseptics, or due to their ineffectiveness, interest has shifted to alternative methods of treatment. One of these methods is the use of honey, which has been used in many cultures for centuries. Since 1990, there has been increased research into the effects of honey. Particular interest has been placed on its antibacterial properties and its potential to treat infections caused by antibiotic-resistant bacteria. This has led to the medicinal use of Manuka honey, which has been shown to have exceptional antibacterial properties. Manuka honey is characterized by the presence of 3-methylglyoxal, which has been shown to be a very effective bactericide, virucide, and fungicide, and is insensitive to temperature changes or enzymatic decomposition. Manuka honey is also very effective against antibiotic-resistant bacteria. There are relatively few reports in the literature on the effect of Manuka honey on bacteria in the oral cavity, with in vivo studies being particularly scarce. The aim of the present study was to compare NSPT with or without additional topical application of Manuka honey. The study also aimed to investigate the impact of periodontitis on the patients' quality of life and the changes associated with etiological treatment of periodontitis. Materials and Methods: This study was designed as a randomized clinical trial comparing the effect of Manuka honey as an adjunct to NSPT versus NSPT without the use of Manuka honey. The clinical parameters, i.e., periodontal pocket depth (PPD), gingival recession (REC), clinical attachment level (CAL), bleeding on probing (BOP), and plaque index (PI) were measured at six sites on each tooth. The polymerase chain reaction method was used for microbiological detection of Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, Prevotella intermedia, Aggregatibacter actinomycetemcomitans, Fusobacterium nulceatum, Parvimonas micra, and Filifactor alocis. Psychometric tests based on Oral Health Impact Profile-14 (OHIP- 14) were used to conduct the analysis of the impact of periodontitis on the quality of life and to assess well-being after the therapy. NSPT was performed according to the standardized protocol by a single operator. After NSPT, subjects were randomly divided into two groups using either a Manuka honey preparation or a placebo preparation. The adjunctive preparation was administered into the periodontal pockets using a specially designed syringe that had identical appearance for both the Manuka and the placebo groups. Periodontal parameters, microbiological findings, and psychometric tests were performed at baseline and after 3 months. Microbiological swabs were additionally taken 7 days after NSPT. Results: No side effects were reported with the use of the Manuka honey or the placebo preparations. NSPT showed a statistically significant decrease in PPD values in both groups after 3 months. In the experimental group, the initial value was 3.63 mm, while after 3 months it decreased to 2.56 mm. In the control group, the initial value was 3.47 mm and decreased to 2.60 mm after 3 months. The proportion of deep pockets (between 5-6 mm) in the experimental group (6.4%) was significantly lower than the one in the control group (8.2%), while the proportion of very deep pockets (with probing depth of > 6 mm) in the experimental group was 0.9%, which is statistically also significantly lower than the one in the control group (2.3%). The reduction of FMBS at 3 months was significantly more pronounced in the experimental group (44.87%) than in the control group (32.66%). After 3 months, the CAL values were 3.12 mm in the experimental group, and 3.06 mm in the control group, with no statistically significant difference between the groups. After 3 months, a statistically significant difference was noted in a higher percentage of closed pockets in the experimental group (78.8%) compared with 69.0% in subjects receiving placebo. After the therapy and the improvement of periodontal status, OHIP-14 values in the experimental group decreased from 19.57 to 11.48, and in the control group from initial values from 19.41 to 14.73 in the experimental group. A statistically significant reduction of periodontopathogenic bacteria A. actinomycetemcomitans, P. intermedia, T. forsythia, and F. alocis was observed in the experimental group compared to the control group. Conclusion: The use of Manuka honey as an adjunct to initial non-surgical therapy could provide additional benefits in terms of elimination of periodontal pockets, improvement of periodontal parameters, alteration of subgingival microbial composition, and the quality of life of patients.