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Research has shown that creating an online learning community is vital in Model-Based Systems Engineering (MBSE) training programs and can be facilitated via the Community of Inquiry (CoI) framework. For professional learners, an online learning community is influenced by their organizational affiliations. The purpose of this research is to explore learning experiences in groups of professional learners with different and homogenous organizational affiliations in an asynchronous online MBSE module. Through the case study methodology, this research examines four sources of data from two cases: Case 1—learners from different organizations (n = 7); and Case 2—overwhelming majority of learners from the same organization (n = 19). Results showed that learners from the same organization reported higher social presence, which, in turn, corresponded to a higher cognitive presence and higher motivation for future MBSE learning. Based on our findings, we recommend that organizations seeking MBSE adoption coordinate with online course providers to create cohorts to participate in the same offerings to facilitate the process of learning community building. We also recommend MBSE course providers facilitate social interaction on multiple communication platforms and create orientation activities for learners from different organizations to promote social presence.