There are immune cell populations differences when comparing CLE and JDM.• JDM had a more prevalent innate immune signature.• CD14+ macrophages are the top immune cell population in JDM;• Interactions between endothelial cells and epithelial cells in DM highlight the skin vasculopathy involved in JDM pathology.• CLE had a higher inflammatory cell infiltrate overall, with increased cell-cell interactions• Microarray confirmed more prominent IFN signature in cSLE compared to DM. Here, IFNA1 is linked to juvenile dermatomyositis.