Food fortification is widely used to address the public health problem of nutrient deficiencies. This study's purpose is to assess the lipid profile and nutritional quality of 13 fortified infant flours (FI) collected “in the field” in Africa and Asia after different periods of storage. The lipid content, fatty acid profiles, lipophilic vitamin content, and lipid oxidation state (peroxide values, secondary oxidation products) are determined. Mycotoxins and packaging materials are also characterized. The lipid content averages 9.1 ± 3.5 g/100 g. Fatty acid profiles are dominated by linoleic (43.3 ± 8.8%), oleic (29.5 ± 7.4%), and palmitic acid (17.8 ± 6.7%) and result in an average ¿6/¿3 ratio of 12.2 ± 5.9 but with high values for some FI. Very high overages in vitamins A, D, and E are observed in products stored for short periods (1–6 months), whereas FI stored for more than 12 months has insufficient vitamin content. Lipid oxidation is acceptable but for six products presenting excessive peroxide values. Most products are contaminated by low amounts of mycotoxins but only two FI do not abide by the regulation. A strong correlation between peroxide values, hexanal content, and time of storage is observed. Practical Applications: The expiration dates for FI commercialized in low-income countries should be shortened from 36 to 12 months so as to guarantee their nutritional quality of these functional foods and to abide by the fortified infant flour legislation. Indeed, FI quality significantly decreases over time of storage. The use of high barrier packaging materials must be generalized, although it is a necessary criterion but not sufficient to ensure the long-term stability of FI. Special attention should be given to reduce lipophilic vitamin overages and to improve their lipid profile, especially the ¿6/¿3 ratio, which has to be lower than 15.