Systemic nature of the human body response to SARS-CoV-2 requires dedicated analysis at the molecular level. COVID-19 during pregnancy affects maternal health and may entail complications in the early neonatal period and possibly long-term consequences for the offspring. The aim of the study was to assess the impact of COVID-19 on amino acid profiles in maternal venous blood, amniotic fluid and umbilical cord blood in order to develop a diagnostic panel accounting for possible consequences. The main group included 29 pregnant patients with a confirmed diagnosis of COVID-19 and the control group included 17 somatically healthy pregnant women. Amino acid profiles of the biological fluids were measured by high-performance liquid chromatography combined to mass spectrometry (HPLC-MS) and assessed in logistic regression models. The analysis revealed altered content of certain amino acids, their biosynthetic precursors and metabolites in the biological fluids collected from patients with COVID-19 possibly reflecting the development of systemic inflammatory reaction and associated changes in gene expression profiles. These findings may guide further research into health outcomes for neonates born from mothers infected with SARS-CoV-2 during pregnancy. The study may help to develop advanced recommendations and differential care protocols for pregnant women and newborns diagnosed with COVID-19.