The aim of this study wasto longitudinally evaluate the undetermined impact of methotrexate (MTX) on the cumulative immunogenicity elicited by three doses of SARS-CoV-2 mRNA vaccination in patients with rheumatoid arthritis (RA). We prospectively evaluated vaccine-induced immune responses following the first dose, 1 and 6months after the second dose, and 1month after the third dose of BNT162b2 or mRNA-1273 in 144 SARS-CoV-2 naïve participants (70 patients with RA, 29 disease controls without immunosuppressive conditions, and 45 healthy controls). Humoral immune responses were assessed by quantifying anti-spike IgG antibody titers and the capacity of circulating antibodies to neutralize the ancestral SARS-CoV-2 strain and the Alpha, Delta, and Omicron variants. Vaccine-induced T-cell responses were measured using an interferon-gamma release assay. At 1 and 6months after the second dose, anti-spike titers were highest in healthy controls, followed by disease controls and patients with RA. Multivariate analyses revealed that MTX treatment was significantly associated with a decrease in anti-spike titers, neutralizing activity, and SARS-CoV-2-specific interferon-gamma levels. Furthermore, MTX dose per body weight was negatively correlated with these two indices of humoral immune response. The third vaccine dose boosted anti-spike titers, especially in patients receiving MTX, while sera from these patients neutralized the Omicron variant far less robustly than those from healthy controls. In conclusion,MTX attenuated immunogenicity following two doses of SARS-CoV-2 mRNA vaccine in patients with RA, particularly resulting in dose-dependent suppression of the humoral immune response. Furthermore, MTX deteriorated the neutralizing activity against the Omicron variant, even after the third immunization.