Immunocompromised patients may be at increased risk to develop COVID-19 during the 2019 β-coronavirus infection. We present the unique opportunity we had to monitor the liver, IL-6 and immune cell course before, during and after COVID-19 in a boy with autoimmune hepatitis (AIH) and type 1 diabetes (T1D). CD4 and CD8 T cells frequencies decreased because of prednisolone, followed by a plateauing increase whereas CD19CD20 B cell increased strongly and was unaffected by COVID-19 infection. Moreover, the percentage of activated CD8 T cells expressing HLA-DR (CD8HLA-DR) increased during COVID-19 and subsided after its clearance. Total regulatory T cells (Tregs: CD4CD25CD127FOXP3) remained stable. Although activated Tregs (CD4CD45RAFOXP3) strongly increased upon prednisolone, it decreased afterwards. Furthermore, regulatory B cells (Bregs: CD19CD20CD24CD38) declined sharply owing to prednisolone. Serum IL-6 remained undetectable at all times. We demonstrated for the first time immune monitoring in a child with AIH and T1D before, during and after COVID-19. We hypothesize that continuing with low level of prednisolone without azathioprine may have abrogated activated Tregs, Bregs and IL-6 production and therefore permitting the activation of CD8 T cells, clearing the virus.