Background Epidemiological data regarding differences in durability and its determinants of humoral immunity following 2– and 3–dose COVID–19 vaccination are scarce. Methods We repeatedly assessed the anti–spike IgG antibody titers of 2– and 3–dose mRNA vaccine recipients among the staff of a medical and research center in Tokyo. Linear mixed models were used to estimate trajectories of antibody titers from 14 to 180 days after the last immune–conferred event (vaccination or infection) and compare antibody waning rates across prior infection and vaccination status, and across background factors in infection–naive participants. Results A total of 6901 measurements from 2964 participants (median age, 35 years; 30% male) were analyzed. Antibody waning rate (per 30 days [95% CI]) was slower after 3–dose (25% [23 – 26]) than 2–dose (36% [35 – 37]). Participants with hybrid immunity (vaccination and infection) had further slower waning rates: 2–dose plus infection (16% [9 – 22]); 3–dose plus infection (21% [17 – 25]). Older age, male sex, obesity, coexisting diseases, immunosuppressant use, smoking, and alcohol drinking were associated with lower antibody titers, whereas these associations disappeared after 3–dose, except for sex (lower in female participants) and immunosuppressant use. Antibody waning was faster in older participants, females, and alcohol drinkers after 2–dose, whereas it did not differ after 3–dose across except sex. Conclusions The 3–dose mRNA vaccine conferred higher durable antibody titers, and previous infection further enhanced its durability. The antibody levels at a given time point and waning speed after 2–dose differed across background factors; however, these differences mostly diminished after 3–dose.