Background Individuals with systemic autoimmune rheumatic diseases (SARDs) are at risk for worse acute and post‐acute COVID‐19 outcomes, though whether individuals with SARDs have longer persistence of viral antigens after COVID‐19 has not been studied. Methods This retrospective cohort study evaluated post‐COVID‐19 differences in SARS‐CoV‐2 antigen (spike, S1, and nucleocapsid) positivity between individuals with SARDs (RheumCARD) and without SARDs (RECOVER‐Adult). SARS‐CoV‐2 antigens were measured in collected samples using a validated ultra‐sensitive single molecule array. This digital enzyme‐linked immunosorbent assay used antibody‐coated magnetic beads to capture antigen molecules, which were loaded into microwell arrays and detected through enzymatic cleavage of a fluorescent substrate. We used logistic regression to estimate unadjusted and adjusted (for age, sex, infection year, vaccination status, and COVID‐19 treatment) odds ratios for SARS‐CoV‐2 antigen positivity at months 3 and 6 following COVID‐19. Results Among 210 individuals with SARDs in RheumCARD and 348 individuals without SARDs in RECOVER‐Adult, any SARS‐CoV‐2 antigen positivity was more common in those with SARDs (36.7% in RheumCARD vs. 18.9% in RECOVER‐Adult; p<0.001). Those with SARDs had higher odds of nucleocapsid antigen positivity (adjusted OR 3.73, 95% CI: 1.28‐10.85) or any antigen positivity (adjusted OR 2.89, 95% CI: 1.43‐5.85) 3 months after COVID‐19 infection and higher odds of nucleocapsid antigen positivity (adjusted OR 6.62, 95% CI: 1.09‐40.30) 6 months after COVID‐19 infection. Conclusion Individuals with SARDs were more likely to have SARS‐CoV‐2 antigen positivity at months 3 and 6 following COVID‐19 infection compared with individuals without SARDs, not explained by demographics, variant, vaccination, or treatment.