Abstract Background The development of questionnaires for primary care practice and research is of increasing interest in the literature. In settings where valuable prior knowledge or preliminary data is available, Bayesian factor analysis can be used to incorporate such information when conducting questionnaire construct validation. This protocol outlines a methodological review that will summarize evidence on the current use of Bayesian factor analysis in the primary care literature. Methods A comprehensive search strategy has been developed and will be used to identify relevant literature (research studies in primary care) indexed in MEDLINE, Scopus, EMBASE, CINAHL, and Cochrane Library. The search strategy includes terms and synonyms for Bayesian factor analysis and primary care. The reference lists of relevant articles being identified will be screened to find further relevant studies. At least two reviewers will independently extract data and resolve discrepancies through consensus. Descriptive analyses will summarize the use and reporting of Bayesian factor analysis approaches for validating questionnaires applicable to primary care. Discussion This methodological review will provide a comprehensive overview of the current use and reporting of Bayesian factor analysis in primary care and will provide recommendations for its proper future use. Systematic review registration PROSPERO CRD42018114978