Studying infant diet and feeding practices through stable isotope analysis provides direct insight into the life and health of vulnerable population groups in the past. Although the general diet in medieval and early modern Livonia has been reconstructed from written sources, little is known about childhood diet during this tumultuous period of Eastern European history. This study presents a comparative investigation of the staple non-adult diet in urban/rural communities during the 13th-17th centuries AD, with a special focus on feeding practices. We aim to reveal the impact of socio-economic circumstances on early childhood nutrition, which affects the physical development and overall survival of this susceptible population group. Bone collagen samples from 176 individuals between the fetal and the 7–15 age categories from four urban/rural South-Estonian cemeteries were cross-sectionally analyzed via EA-IRMS (Elemental Analysis with Isotope Ratio Mass Spectroscopy) for δ13C and δ15N. Results suggest that South-Estonian children had a staple terrestrial C3 diet integrated with animal proteins. Significant divergences were observed between urban and rural sites and slight variation occurred among rural subgroups, possibly resulting from a wider food choice available in towns, different consumption of C4 foods, and/or secular changes. This study provides the first data regarding infant feeding practices in medieval and early modern Livonia. These practices were similar among the different contexts, indicating comparable cultural traditions in child rearing. Breastfeeding was likely practiced for 1–2 years, with supplementary foods introduced around 1 year of age. The weaning process was probably concluded around the age of 3. The δ13C and δ15N values of older children are comparable to those of the adults from the same sites, indicating their diets became similar after weaning, when they started working and obtained a more mature social status.