Context: Manuscript management systems (MMS) serve as centralized platforms for managing the submission, review, and publication of scholarly articles, thereby streamlining the publishing process. The submission process is crucial for usability analysis, as it represents the initial stage of interaction with users’ profiles. While many researchers emphasize the importance of making these systems more user-friendly, there is a notable lack of studies evaluating the user experience of prominent MMS and offering solutions for identified usability issues. Aim: This research aims to identify usability issues faced by authors working with prominent manuscript management systems, measure user satisfaction levels for the evaluated systems, and propose usability guidelines to enhance their user experience. Method: In this research, the authors conducted comparative usability testing to identify usability issues encountered by typical users when interacting with prominent manuscript management systems. Additionally, they utilized the SUS questionnaire to measure user satisfaction with the submission process. Results: The usability testing results reveal that Editorial Manager, ScholarOne, and Open Journal Systems exhibit numerous usability issues in submission, user registration, password recovery, and profile updating. These issues violate several usability heuristics and web design principles. The results indicate low user satisfaction, with Editorial Manager rated as “Awful,” ScholarOne as “Okay,” and Open Journal Systems as “Poor”. Conclusion: Usability analysis identifies key usability issues and proposes usability guidelines for manuscript management systems. These guidelines aim to minimize usability issues and ensure excellent user experience, thereby enabling developers to design more usable manuscript management systems.