Peripheral blood inflammatory profiles are increasingly well characterised in Covid-19 but knowledge of the host response within inflamed tissues is lacking. Post-mortem lung and spleen whole-tissue proteomics identified differentially abundant proteins of mechanistic and translational interest (including MCP-3, TYMP, EN-RAGE and CSF-1). Lung proteomic clusters identified distinct disease stages that differed in pulmonary viral presence, inflammation severity, illness duration, and abundance of proteins of interest including IL-6 and IRAK1