Emerging studies indicate that some COVID-19 patients suffer from persistent symptoms including breathlessness and chronic fatigue; however the long-term immune response in these patients presently remains ill-defined. Here we describe the phenotypic and functional characteristics of B and T cells in healthy individuals and individuals with acute or convalescent COVID-19. We report that the alterations in B cell subsets observed in acute COVID-19 patients were largely recovered in convalescent patients. In contrast, T cells from convalescent patients displayed long-term alterations with persistence of a cytotoxic programme evident in CD8+ T cells as well as elevated production of type-1 cytokines and IL-17. Interestingly, B cells from patients with acute COVID-19 displayed an IL-6/ IL-10 cytokine imbalance in response to toll-like receptor activation, skewed towards a pro-inflammatory phenotype. Whereas the frequency of IL-10+ B cells was restored in a subset of convalescent patients, IL-6 production remained elevated. Our data are the first to define long-term alterations in the lymphocyte compartment of previously hospitalized COVID-19 patients, at up to 19 weeks of convalescence, and identify 3 subgroups of convalescent patients based on distinct lymphocyte phenotypes. We propose that alterations in B and T cell function following hospitalisation with COVID-19 could impact long-term immunity and contribute to some persistent symptoms observed in convalescent COVID-19 patients.