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Scope Lack 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 results An 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. Conclusions This 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., This work was supported by the projects PG2018-096608-B-C21(Spanish Ministry of Science and innovation (MCIN). Generación delConocimiento. MCIN/ AEI /10.13039/501100011033/ FEDER “Una man-era de hacer Europa”), UHU-1256905 and UHU-202009 from the FEDERAndalusian operative program (Ministry of Economic Transformation, In-dustry, Knowledge and Universities, Andalusia, Spain), and a researchgrant from Fundación La Marató-TV3 (MilkCORONA, ref 202106). FJSCthanks Junta de Andalucía and University of Huelva for a predoctoralcontract (Ref. SNGJ5-TS-005, Garantía Juvenil). Funding for open accesscharge: Universidad de Huelva / CBUA. The authors are grateful to FEDER(European Community) for financial support through grants UNHU13-1E-1611 and UNHU15-CE-3140. The funding sources had no role in the de-sign and conduct of the study; collection, management, analysis, and in-terpretation of the data; preparation, review, or approval of the manuscript;and decision to submit the manuscript for publication