Full spectrum flow cytometry has facilitated in-depth studies in the characterisation of the immune system in health and disease. Sample analysis can be performed with a large number of markers in one single tube. This is an important consideration when analysing clinical samples where the sample size is limited and/or where little is currently known about the disease, such as SARS-CoV-2 infection. In this study, we describe the optimisation and analysis of a 35-colour panel designed by Cytek Biosciences, for the in-depth analysis of immune cell populations in samples of patients exposed to SARS-CoV-2 infection. The panel presented here identifies several immune cell subsets, both within the lymphoid (conventional and regulatory CD4 T cells, CD8 T cells, γδ T cells, NK cells, NKT-like cells, B cells, ILC) and myeloid cell compartment (basophils, monocytes and dendritic cells). The inclusion of additional markers (activation and differentiation markers, chemokine receptors) allows to further characterise each immune cell population. This panel will permit us to further investigate long-term immunity against SARS-CoV-2 and determine whether disease severity affects the immune system over time. For this, we have collected and cryopreserved peripheral blood mononuclear cells from 15 patients at 3 and 12 months post non-lethal infection. A fully automated computational analysis strategy was undertaken consisting of an unsupervised approach using both dimensionality reduction and clustering algorithms and an internal healthy control control was included in each run to ensure consistency within runs. Our results show that the global immune compartment is stable and consistent over time independent of the disease severity and the T cell phenotype observed in patients exposed to SARS-CoV-2 is maintained over 12-months period.