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The communities of Puerto Rico are highly vulnerable to climate change as the archipelago has experienced a multitude of compounding crises and extreme weather events in recent years. To address these issues, the research, analysis, and design of grand challenge solutions for disaster-prone regions like Puerto Rico can utilize collaborative transdisciplinary efforts. Local non-governmental and community-based organizations have a pivotal role in the reconstruction processes and the building of community and environmental resilience in underserved communities. This paper contributes an empirical case study of an online transdisciplinary collaboration between a group of academics and a Puerto Rican non-governmental organization, Caras con Causa. From participant observation, it includes a document analysis of meeting notes with cohort members who were involved in a collaborative National Science Foundation Project, The INFEWS-ER: A Virtual Resource Center Enabling Graduate Innovations at the Nexus of Food, Energy, and Water Systems, with Caras con Causa between October 2020 and April 2021. Caras con Causa focuses on uplifting Puerto Ricans by creating and administering environmental, educational, economic, and community programs, highlighting disaster relief and resilience to help Puerto Rican food, energy, and water systems. Eight key discussion themes emerged from the document analysis: team organization, collaboration with Caras con Causa, deliverables, team contributions, context understanding, participation outcomes, technology setup, and lessons learned. We analyze each of the emerging themes to explain how academics may use transdisciplinary skill sets in addition to standard disciplinary-based approaches or techniques to enhance the institutional capacity of a non-governmental organization doing community resilience work to benefit local food, energy, and water systems. While the learned lessons in this non-governmental organization-academic collaboration may be context-specific, we provide insights that may be generalizable to collaborations in comparable transdisciplinary settings.