Critical appraisal is a core component of JBI qualitative evidence synthesis, offering insights into the quality of included studies and their potential influence on synthesized findings. However, limited guidance exists on whether, when, and how to exclude studies based on appraisal results. This study examined the methods used in JBI qualitative systematic reviews and the implications for synthesized findings. In this study, a systematic analysis of qualitative reviews published between 2018 and 2022 in JBI Evidence Synthesis was conducted. Data on decisions and their justifications were extracted from reviews and protocols. Descriptive and content analysis explored variations in the reported methods. Forty-five reviews were included. Approaches reported varied widely: 24% of reviews included all studies regardless of quality, while others applied exclusion criteria (36%), cutoff scores (11%), or multiple methods (9%). Limited justifications were provided for the approaches. Few reviews cited methodological references to support their decisions. Review authors reported their approach in various sections of the review, with inconsistencies identified in 18% of the sample. In addition, unclear or ambiguous descriptions were also identified in 18% of the included reviews. No clear differences were observed in ConQual scores between reviews that excluded studies and those that did not. Overall, the variability raises concerns about the credibility, transparency, and reproducibility of JBI qualitative systematic reviews. Decisions regarding the inclusion or exclusion of studies based on critical appraisal need to be clearly justified and consistently reported. Further methodological research is needed to support rigorous decision-making and to improve the reliability of synthesized findings.