Background Conventional antifungal therapies, including topical applications, are effective against oral candidiasis but have limitations such as resistance development and cytotoxicity especially for immunocompromised patients. Phytotherapy presents a promising alternative, offering potential solutions to these challenges. However, despite numerous clinical trials, there is a lack of standardized protocols for phytotherapeutic applications. This systematic review protocol seeks to evaluate the potential of phytotherapy as an alternative treatment for oral candidiasis and compare its efficacy with standard antifungal therapies. Protocol This protocol aims to assess the effectiveness of phytotherapy compared to standard antifungal treatments for oral candidiasis. Initially, controlled descriptors in MeSH terms (e.g., “Candidiasis, Oral,” “Phytotherapy”) and keywords were selected from MEDLINE and combined using Boolean operators (‘AND’, ‘OR’) to create a comprehensive search strategy. Titles and abstracts will be screened by two independent reviewers to select studies that meet the inclusion criteria. The quality and risk of bias of the selected studies will be assessed afterward. Data will be gathered using standardized tools and subsequently synthesized for analysis. Discrepancies between reviewers will be settled through discussion, or, if required, by involving a third reviewer. Discussion Results obtained from this systematic review will describe various natural compounds like essential oils, herbal extracts, and bioactive plant ingredients that exhibit antifungal properties used against oral candidiasis and will evaluate their effectiveness in comparison to standard antifungal treatments. Systematic review registration PROSPERO: CRD42024584029 (Registered on 07/09/2024)