With a strong demand for online education and project management in deeper scope and larger scale to better fit COVID-19 pandemic situation, exploring new knowledge of online education to make it more effective became vital with the new challenges of STEM education. To resolve the above problem, this paper focuses on various aspects of online STEM education project management where the Enhanced Noyce Explorers, Scholars, Teachers (E-NEST) three-tiered structure was implemented during the COVID-19 period. Two City University of New York (CUNY) institutions, New York City College of Technology (City Tech) and Borough of Manhattan Community College (BMCC) used the three-tiered structure referred to as Explorer, Scholar and Teacher which incorporated advancements in teaching internships, professional development workshops and mentorships remotely. Built upon the theories of engagement, capacity and continuity (ECC) and team-based learning (TBL), this remote learning model and infrastructure had a positive impact on STEM education and project management. The technological tools utilized included Zoom, Google Meet, Microsoft teams, Blackboard Collaborate Ultra, Skype and SurveyMonkey. The results from qualitative and quantitative data including project evaluation, online surveys and focus group interviews demonstrate that the modified remote learning and management tools were effective. This indicated that the E-NEST model greatly supported student success and faculty in online learning and project management meetings. The E-NEST STEM education project was compared to two other project management models along with the previous NEST curriculum. Faculty emphasized practicing project management proactively and utilized best practices of classroom and time management consistent with Project Management Body of Knowledge (PMBOK) and Project Cycle Management (PCM) guidelines. The comparisons attest that the E-NEST project developed excellent and innovative online platforms for student learning with project management and ECC and TBL applications. Hereafter, this research can be used to constructively develop more online STEM education learning models and platforms and integrate new practice and technology globally. These ideas can contribute to future research that could be applied internationally to STEM education projects in K-12 and higher education institutions.