B cells are considered to play a major role in the pathogenesis of multiple sclerosis (MS), as many successful therapeutics remove them from circulation. One such disease-modifying therapy is alemtuzumab, a monoclonal antibody that depletes CD52+ cells and is thought to reset the immune system without the need for ongoing therapy in a proportion of patients. What is not yet known is the exact cell subsets that contribute to disease pathogenesis and the disease quiescence induced by alemtuzumab. We utilised mass cytometry to analyse the B cell repertoire of relapse-remitting MS (RRMS) patients before and after alemtuzumab treatment. Blood was collected from RRMS patients either before, < 12 months or > 12 months after alemtuzumab treatment. Blood was also taken from RRMS patients during relapse. The R package ‘Spectre’ was used to assist in the computational analysis of these data. FlowSOM clustering identified a range of B cell subsets across patients, with sparse partial least squares-discriminant analysis (sPLS-DA) and permutational multivariate analysis of variance (PERMANOVA) showing a difference in the overall B cell repertoire between groups. IgA+ and IgG1+ B cells were found to differ between groups, including an increase in IgG1+ B cells during relapse. BLNK, CD40 and CD210 expression by total CD19+ B cells were also at a lower level in RRMS patients compared to non-MS controls, with similar results at the transcriptomic level in a separate RRMS cohort. Finally, alemtuzumab restored BLNK, CD40 and CD210 expression by IgA+ and IgG1+ B cells, which was altered again during relapse. These data suggest impairment of IgA+ and IgG1+ B cells may contribute to MS pathogenesis, which can be restored by alemtuzumab.