Secretory Immunoglobulin A (SIgA) in human milk plays a central role in complex maternal-infant interactions that influence long term health outcomes. Governed by genetics and maternal microbial exposure, human milk SIgA shapes both the microbiota and immune system of the infant. Historically, SIgA-microbe interactions have been challenging to unravel due to their dynamic and personalized nature, particularly during early life. Recent advances have helped to clarify how SIgA acts beyond simple pathogen clearance to help guide and constrain a healthy microbiota, promote tolerance, and influence immune system development. In this review, we highlight these new findings in the context of the critical early-life window and propose outstanding areas of study that will be key to harnessing the benefits of SIgA to support healthy immune development in infancy.