This systematic review focuses on the different study protocols on CoQ10 as an adjunct in non-surgical periodontitis therapy. The study protocol was developed following PRISMA guidelines and was registered in PROSPERO (CRD42021156887). A sensitive search up to January 2022 considered MEDLINE via PubMed and Web of Science, Embase, Web of Science Core Collection via Web of Science, Google Scholar, Cochrane CENTRAL, WHO (ICTRP), ClinicalTrials.gov, and grey literature. Randomized controlled (SRP with/without placebo) clinical trials (RCTs) on all types of CoQ10 administration were included. The primary outcome was probing pocket depth (PPD). Secondary outcomes were bleeding on probing, clinical attachment loss, and gingival and plaque indices. Twelve RCTs with local and five with systemic CoQ10 administration were included. The study protocols were heterogeneous. Local CoQ10 administration was performed once or several times in a period up to 15 days. Systemic CoQ10 was applied twice or three times daily for six weeks up to four months. The reporting quality was low, including missing information about CoQ10 doses. Risk of bias was high or unclear. About half of the studies reported significant group differences for PPD. Until now, no statement on the effectiveness of CoQ10 in non-surgical periodontitis therapy is possible. Further high-quality RCTs are necessary and should consider the protocol recommendations of this review.