The EL-BONGO physics project aims to revolutionize higher education in Latin America through digital transformation, emphasizing virtual research and learning communities, and open science practices. It builds upon the success of the LA-CoNGA physics program, seeking to establish a network of research communities across Central America and the Andean region, involving 18 Latin American and European universities from nine countries. The project collaborates with prominent research centers, industrial partners, and multilateral organisations.Key objectives include promoting collaboration through digital platforms, promoting digital education and open science, and developing practical skills in digital fabrication. The project also focuses on implementing a hybrid Bologna Master Program. Four Physics Research and Learning Communities will be established in High Energy Physics, Space Weather, Seismology and Earth Hazards, and Artificial Intelligence. Innovative digital learning methods, research internships, and social impact activities like hackathons will enhance educational experiences and bridge academic research with real-world problems.The project also aims to establish a collaborative Science Gateway for science and education, utilizing advanced digital infrastructure to overcome geographical and socio-economic barriers. The Digital Science Gateway Hub will provide access to educational resources, support networking and collaboration, and enhance the visibility and dissemination of research findings. The project's work plan is structured into six work packages covering preparation, development of tools, training, quality assurance, dissemination, and project management, with specific responsibilities allocated to participating institutions. Universidad Antonio Nariño, in Colombia, will lead the project along with the collaboration of Université Paris Cité as co-pi, facilitating knowledge transfer and collaboration between Europe and Latin America.