The aim of this study was to assess the impact of SARS-CoV-2 infection during pregnancy on the molecular profile of human milk and to identify associations between the expression of regulatory genes and clinical parameters of newborns. The study included a group of 19 women who had COVID-19 during pregnancy and a healthy control group of 21 women. Expression levels of miR-21, miR-155, and the transcription factor SOX1 were determined in human milk using qPCR. The correlation of SOX1 expression with parameters in cord blood and infant blood was also analyzed. It was shown that maternal SARS-CoV-2 infection (during pregnancy) is associated with significantly higher levels of miR-21, miR-155, and SOX1 expression in human milk. Furthermore, strong statistical correlations were found in the study group: SOX1 expression was positively correlated with C-reactive protein (CRP) levels and lactate concentration (LAC) in arterial umbilical cord blood, while negatively correlated with glucose levels. Our research shows that SARS-CoV-2 infection during pregnancy induces changes in the molecular composition of early breast milk, promoting immunomodulatory (miR-155) and regenerative (miR-21, SOX1) molecules. Post-COVID-19 breast milk serves as an active biochemical communication system, providing the newborn with signals that may modulate adaptive and immune responses to the unfavorable intrauterine environment.