Soy infant formulas (SIF) have long been used as an alternative for infants with special nutritional requirements. However, the medical indications for their use, their allergenicity, safety and efficacy are still controversial. To present recommendations for the use of SIF based on the existing literature. We consulted systematic reviews and clinical practice guides, through validated search algorithms, and systems such as Appraisal of Guidelines for REsearch and Evaluation (AGREE)II and Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). For the elaboration of the clinical recommendations, the most important topics were analyzed and discussed by the responsible researchers and the group of experts in the development of a position paper. The quality of the evidence was evaluated using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) system. Several reports with variable quality of evidence were found. They support SIF's efficacy in the management of cow's milk allergy and infant's digestive tolerance, as well as its low cross allergy compared to cow's milk and other formulas. We also found other studies that indicate the safety of SIFs on different nutritional, immune and developmental parameters. There is also evidence that demonstrates that SIFs have important advantages in terms of cost-benefit, palatability and effects on the intestinal microbiota, compared to other formulas. Although evidence to recommend its use in functional digestive disorders is limited, SIFs have an adequate safety profile and are still a valid option for infant feeding.