Background: In Mexico, the fortification of corn and wheat flours with iron, zinc, and folic acid and the restoration of B-vitamins is a mandatory program. However, the monitoring and evaluation (M&E) of this fortification process is not well understood. Thus, the purpose of the study was to understand the M&E of the food fortification program in Mexico, with an emphasis on technology research and development. Methods: Open-ended exploratory interviews were conducted with food technology representatives (n = 9), food science academic faculty (n = 1), president of a private tortilla-making federation (n = 1), and representatives of the federal monitoring agency (n = 2). Interviews were transcribed and themes were identified using the content analysis methodology. Inter-rater reliability was assessed by calculating an intraclass correlation coefficient (ICC) between the raters (n = 3). Results: A total of 49 codes were identified that resulted in three overarching themes, manufacturing/processing, monitoring logistics, and nutrition. Overall, there is a need for more robust internal and external M&E with Mexico’s fortification program to improve the manufacturing/processing of fortifying the tortillas, the monitoring of this fortification program, and the impact the fortified tortillas have on the nutritional status of the Mexican population. The overall ICC was 0.87. Conclusions: The present study can be used to gain insight into Mexico’s fortification program and to inform food fortification policymakers of best practices.