ScopeLack of information about the impact of maternal severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection on the elemental and metabolomic profile of human milk (HM).Methods and resultsAn observational study on HM from mothers with COVID‐19 is conducted including a prepandemic control group. Maternal–infant clinical records and symptomatology are recorded. The absolute quantification of elements and untargeted relative metabolomic profiles are determined by inductively coupled plasma mass spectrometry and gas chromatography coupled to mass spectrometry, respectively. Associations of HM SARS‐CoV‐2 antibodies with elemental and metabolomic profiles are studied. COVID‐19 has a significant impact on HM composition. COVID‐19 reduces the concentrations of Fe, Cu, Se, Ni, V, and Aluminium (Al) and increases Zn compared to prepandemic control samples. A total of 18 individual metabolites including amino acids, peptides, fatty acids and conjugates, purines and derivatives, alcohols, and polyols are significantly different in HM from SARS‐CoV‐2 positive mothers. Aminoacyl‐tRNA biosynthesis, phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine, and linoleic acid pathways are significantly altered. Differences are obtained depending on COVID‐19 symptomatic and asymptomatic status.ConclusionsThis study provides unique insights about the impact of maternal SARS‐CoV‐2 infection on the elemental and metabolomic profiles of HM that warrants further research due the potential implications for infant health.