A better understanding of the practical and methodological challenges inherent in accurately tracking female hormonal status would enhance the clarity of research findings in exercise metabolism. The purpose of this study was to conduct an objective assessment of the quality of existing literature in this area and to provide a general overview of the practical conditions and issues encountered in studies investigating substrate metabolism during exercise in women, both in those using (HC+) or not using (HC−) hormonal contraceptives. Forty-four articles were identified through systematic reviews, meta-analyses, and searches on PubMed/MEDLINE. A quality assessment framework was developed and applied using a double-blind scoring approach. The loss/exclusion of data between baseline and final analyses per study was quantified, and the main challenges were highlighted. A higher mean global score was observed in studies conducted among HC+ women (81%) than those among HC− women (46%). Although the dropout rates were rarely mentioned in HC+ women articles, the mean rate of participant/data loss in HC− groups was 22.1%. The rate of HC− participant loss was positively correlated with the global score (r = .504, p = .02). High-quality research may be easier to achieve in studies involving HC+ women compared with those involving HC− women. Studies on HC− women seem to face more practical challenges, such as tracking the menstrual cycle and targeting specific (sub)phases of the menstrual cycle, along with technical and feasibility limitations. Thus, although the framework for designing such studies exists, the quality assessment of the available literature emphasizes its challenge in terms of research implementation.