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Scientific research is the main driver to push forward and disseminate botanical knowledge. Despite many institutions having this fundamental aim as a core activity, many of them do not have a complete set of facilities, expertise, staff, and resources to cover all the steps involved in the study, management, conservation, and popularization of plant diversity. Accordingly, we propose a workflow formalizing the cooperation between a botanical garden and a botanical research center, focused on the study of plant endemic species. Specifically, the cooperation was implemented between the PLANTSEED Lab of the Department of Biology and the Botanic Garden and Museum of the University of Pisa. We present seven representative case studies (Armeria arenaria complex, Bellevalia webbiana, Crocus etruscus and C. ilvensis, Dianthus virgineus complex, Pulmonaria hirta complex, and Santolina chamaecyparissus complex) to disentangle the approaches and opportunities arising from cooperative approaches, from laboratory to cultivation. We analyze the emerging properties derived from this synergistic cooperation by promoting open research questions and answering them using a comprehensive approach to improving endemic plant species research, conservation, and popularization in the botanical garden. In this manuscript, we show how a cooperative approach between heterogeneous botanical institutions can constitute an effective and easy-to-implement approach to achieve the goals of each partner involved in the cooperation.