Objective The peripheral lymphocyte compartment of patients with primary Sjögren’s syndrome (pSS) differs strongly from healthy individuals. Whether this altered lymphocyte composition also changes abnormally during immune reactions, especially by novel CoV-2-vaccines, is unknown. Methods Peripheral blood mononuclear cells (PBMC) from 26 pSS patients and 6 healthy controls were compared before Coronavirus-2 (CoV-2) vaccination (Pfizer/BNT162b2, Moderna/mRNA-1273, AstraZeneca/AZD122 ChAdOx1 nCoV-19) and 7 days after secondary vaccination. Spike 1 (S1)-receptor binding domain (RBD)-specific IgG antibodies were measured in serum samples. Among PBMCs, B and T cell subpopulations were phenotypically analysed and RBD-specific B and plasma cells were evaluated. Results Immunisation induced CoV-2 specific serum antibodies in all pSS patients and healthy participants. When analysing pSS patients and controls together, frequencies of circulating IgG+ RBD-specific antibody-secreting cells (ASC) and anti-RBD serum titres correlated (r=0.42, p=0.022). Previously described alterations of peripheral B cells in pSS patients (e.g. reduced memory B cells, increased naive and transitional B cells and higher maturity of ASCs) remained stable during vaccination. The subset distribution of CD4+ and CD8+ T cells also stayed largely unchanged. However, frequencies of CD4+CXCR5-PD-1+ circulating peripheral helper T (cTPH)-like cells increased in pSS patients comparing pre- and post-vaccination (p=0.020), while circulating CD4+CXCR5+PD-1+ follicular helper T (cTFH)-like cells declined (p=0.024). Conclusion An immune reaction induced by vaccination with the novel CoV-2 vaccines yields adequate antibody production and vaccine specific lymphocytes in pSS patients and controls. Aberrant lymphocyte subset distribution in pSS patients persisted after vaccination and no major changes were induced despite small changes in cTPH and cTFH cells.