Being endowed with vast agricultural resources, the University of Southern Mindanao has great potential to develop R&D outputs for food security, systems, and innovations. A futures thinking mindset provides a framework for envisioning how USM’s research efforts can be harnessed to ensure food security in a range of possible future scenarios. To this end, the USM Futures Thinking Program implemented a series of capacity building activities that commenced in March 2021. Guided by consultations with the Philippine Futures Thinking Society (PhilFutures) and the office of Senator Pia Cayetano, three workshops were conducted. The first workshop was the 2-day Futures Thinking MasterClass, which was attended participants from USM and from other agencies in Region XII. The second and third workshops were Scenario and Strategy Development, and Moonshot Thinking Innovation Lab. These workshops were attended by selected USM faculty. Through the workshops, the USM Futures Thinking Team was formed and consisted of four groups: CornLai Futurists for cereals, Cacao Futurists for high-value crops, Halal Futurists for Halal products and Protein for Peace Futurists for protein sources. These teams underwent a series of brainstorming activities to develop proposals on food futures for possible external funding. Thirteen R&D projects and eight extension initiatives were produced, and these were presented to the USM Research, Development, and Extension Committee (URDEC) for evaluation. Through participation in the Futures Thinking program, USM faculty proponents discovered how a futures thinking mindset can generate strategies for crafting new research proposals and taking appropriate actions towards food security and sustainability.