In this preprint, Rodriguez et al. used mass cytometry and Olink to longitudinally profile immune cells and protein biomarkers in the blood of 39 patients with severe COVID-19 from acute infection to recovery. Partition-based graph abstraction identified IFNγ-induced CD62L+ eosinophils, which appeared 2–6 days after hospitalization. In addition, the authors highlight a correlation between IgG responses and circulating basophil numbers. Finally, integrating 148 plasma proteins and 63 immune cell populations in a multi-omics factor analysis identified potential cellular and plasma biomarkers of transition to recovery from severe COVID-19. This work supports further investigation into the role of eosinophils in lung hyperinflammation and the potential role of basophils in enhancing the humoral response to COVID-19.