Micronutrient deficiencies remain a significant public health issue in Southeast Asia, particularly in vulnerable populations, such as women of reproductive age and young children. An important nutrition-specific intervention to address micronutrient malnutrition is fortification of staple foods and condiments. In October 2013, the International Life Sciences Institute (ILSI) Southeast Asia Region held a workshop on micronutrient fortification of food in Bangkok, Thailand. The objective was to engage multiple stakeholders in a discussion on food fortification and its importance as a public health intervention in Southeast Asia, and to identify and address key challenges/gaps in and potential opportunities for fortification of foods in ASEAN countries. Key challenges that were identified include: “scaling up” and mobilizing sustainable support for fortification programs in the form of multi-stakeholder partnerships, effecting policy change to support mandatory fortification, long-term monitoring of the programs’ compliance and efficacy in light of limited resources, and increasing awareness and uptake of fortified products through social marketing campaigns. Future actions recommended include the development of terms of engagement and governance for multi-stakeholder partnerships, moving towards a sustainable business model and more extensive monitoring, both for effectiveness and efficacy and for enforcement of fortification legislation.